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Indonesia Cruises

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Small ship cruises in Indonesia offer abundant activities and sights, including snorkeling in crystal-clear waters, exploring villages, and spotting wildlife. Sail by traditional villages set against a backdrop of dramatic limestone cliffs on Misool; swim with manta rays and dolphins around Komodo Island; and explore the lush jungles of Bali. The best part is that you can do all this while enjoying the comfort and excellent service of a small ship cruise. The best time for an Indonesia cruise is now! Our Indonesia cruises start from $5,825 to $79,000 for cruises of 8 to 24 days days. Contact us to advise which one suits you best and start planning your trip.
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    • Indonesia
Stand up paddling
from $6,800
EXPLORE

Raja Ampat Liveaboard Kayak Adventure

Small Group Tour - 12 Day Itinerary aboard Jakare
  • Sail to Raja Ampat in Indonesia
  • Witness Segaf Islands' azure waters
  • See Wayil Island white-sand beach
  • Visit Balbulol Island lagoon
  • Explore Gam Island marine life
  • Enjoy different water activities
  • Kayak in Raja Ampat on your beach v
Starts / Ends
Sorong / Sorong
Activities
Land & Sea Exploration
Activity Level
Easy Active
Discover the Raja Ampat Islands, West Papua on a 12-day cruise aboard Jakare. Explore tiny islands and dive into activities like kayaking, diving, snorkeling, and SUP. Enjoy adventure and relaxation in one of the world's most stunning locations.
Cruise Details
0
Cruising Adventures! Banda Islands
from $10,050
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SeaTrek The East Indies on a Spice Island Exploration

Maumere-Ambon - 12 Day Itinerary aboard Katharina
  • Visit Laratuka's unique churches
  • Explore the Forgotten Islands
  • Snorkel in crystal-clear water
  • Discover Indonesia’s Ring of Fire
Starts / Ends
Maumere / Ambon Island
Activity Level
Variable
Departing from Maumere, this exciting 12-day South Pacific cruise on Katharina visits the remote Banda Islands, where you can wander through the nutmeg plantations before retracing ‘the marine spice route’ north through the Moluccan Islands to the clove plantations of the fabled Sultanate of Ternate.
Cruise Details
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Wild Komodo Dragon in its habitat
from $5,825
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Whale Sharks, Corals & Dragons

Komodo-Komodo - 9 Day Itinerary aboard Ombak Putih
  • Visit local communities
  • Snorkel along vibrant coral reefs
  • Enjoy a barbecue on the beach
  • Discover unique species
Starts / Ends
Komodo Island / Melo Village
Activity Level
Variable
Spend nine days snorkeling, encountering wildlife, and exploring tropical islands while cruising along Komodo and back aboard Ombak Putih. Begin your journey on Komodo Island and see the Komodo dragons, snorkel on Komodo Park’s best reefs, swim with manta rays, and more. Then visit Rinca Island, which is known for its diverse wildlife.
Cruise Details
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Komodo Dragons at Komodo National Park Indonesia
from $8,800
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Orangutans and Dragons

Bali - Komodo - 14 Day Itinerary aboard Katharina
  • Learn about Orangutans in Borneo
  • Visit a Dayak community
  • See volcanoes and Komodo dragons
Starts / Ends
Bali / Melo Village
Activity Level
Variable
Embark on a 14-day, two-part cruise aboard Katharina and explore the rich wildlife and cultural heritage of Indonesia. Explore Borneo and visit an orangutan conservation center and a local Dayak village. Return to Bali and set sail to various islands, exploring the highlights of Komodo along the way.
Cruise Details
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Cruising Adventures! Orangutan
from $8,800
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Orangutans and Dragons

Bali-Komodo - 13 Day Itinerary aboard Ombak Putih
  • Visit a Dayak community
  • Learn about orangutans in Borneo
  • Snorkel over vibrant coral reefs
  • Spot Komodo dragons
Starts / Ends
Borneo / Melo Village
Activity Level
Variable
Embark on a 13-day, two-part cruise aboard Ombak Putih and explore the rich wildlife and cultural heritage of Indonesia. Explore Borneo and visit an orangutan conservation center and a local Dayak village. Fly to Bali and set sail to various islands, exploring the highlights of Komodo along the way.
Cruise Details
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Mountain Range in Komodo National Park, Indonesia
from $5,825
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Whale Sharks, Corals & Dragons

Komodo-Komodo - 9 Day Itinerary aboard Katharina
  • Visit local communities
  • Snorkel along vibrant coral reefs
  • Enjoy a barbecue on the beach
  • Discover unique species
Starts / Ends
Komodo Island / Melo Village
Activity Level
Variable
You spend nine days cruising round‑trip from Komodo on board Katharina, seeing Komodo dragons, whale sharks, manta rays, and coral reefs. You snorkel on the reefs, swim with marine animals, and visit islands with diverse wildlife.
Cruise Details
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A group of local villagers playing traditional instruments in Forgotten Islands, Indonesia
from $16,060
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Spice Islands & Forgotten Islands Expedition

Ambon to Labuan Bajo - 12 Day Itinerary aboard Aqua Blu
  • Explore historic spice route
  • Meet indigenous island tribes
  • Experience Wetar Island
  • Hammerhead encounter at Nyata
Starts / Ends
Ambon Island / Labuan Bajo
Activities
Festival Visits, Fishing
Activity Level
Variable
Discover Indonesia’s remote Spice Islands and Forgotten Islands on a 12-day expedition from Ambon to Labuan Bajo aboard Aqua Blu. Snorkel coral reefs, explore historic forts, meet local communities, and experience the beauty and culture of these rarely visited islands.
Cruise Details
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Explore the culture of Indonesia
from $16,395
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Raja Ampat & Spice Islands

Darwin to Sorong - 19 Day Itinerary aboard Coral Geographer
  • Visit Banda Neira fort
  • Snorkel at Seram and Besar Islands
  • Meet local artisans in Tumbur
  • Chance to swim with whale sharks
Starts / Ends
Darwin / Sorong
Activity Level
Variable
Set sail on a 19-day cruise aboard Coral Geographer from Darwin through Indonesia’s Spice Islands and Raja Ampat, famed for their ancient cultures, historic forts, and incredible biodiversity. This adventure blends cultural insights and natural wonders.
Cruise Details
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Northern Common Cuscus in Sorong, Indonesia
from $8,100
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Jewels of Raja Ampat

Roundtrip Sorong - 10 Day Itinerary aboard Katharina
  • Swim through Tomolol’s Cave
  • Trek in Batanta Island's jungle
  • Discover pristine coral reefs
  • Visit Aljui Bay's Pearl Farm
Activity Level
Variable
Join the Katharina on this exceptional 10-day Jewels of Raja Ampat cruise roundtrip Sorong to explore incredible landscapes and sail across one of the most desired destinations in the world, Indonesia. Relax in this region's natural temples, beaches, and wildlife immersion through snorkeling and kayaking.
Cruise Details
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Wajag Island, Raja Ampat
from $15,295
EBD
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Living Treasures of Raja Ampat & the Spice Islands

Roundtrip Denpasar - 13 Day Itinerary aboard Greg Mortimer
  • Visit Wayag Island lagoon
  • Explore Raja Ampat
  • Hike Mount Pindito
  • Discover Banda Neira’s history
Starts / Ends
Denpasar / Sorong
Activities
Photography Seminars
Activity Level
Variable
Arrive in Bali to begin your 13-day journey, then fly to Sorong for embarkation aboard the Greg Mortimer to explore Raja Ampat and the Moluccas. This trip combines adventure and cultural experiences, with opportunities for diving, birdwatching, and visiting remote villages and historical sites.
Cruise Details
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Colorful sunset over Sulawesi
from $9,490
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Island Empires & Ancient Mariners

Darwin to Makassar - 15 Day Itinerary aboard Coral Geographer
  • Explore Komodo Island wildlife
  • Trek Padar Island peak
  • Snorkel vibrant coral reefs
  • Swim Pink Beach waters
Starts / Ends
Darwin / Makassar
Activities
Local Market Visits, Hiking, Scuba Diving, Urban Exploration
Activity Level
Variable
Embark on a 15-day cruise through Indonesia aboard Coral Geographer. Explore remote islands, see Komodo dragons, climb Padar Island, witness unique dances, and experience Toraja culture. Swim, snorkel, kayak, and visit traditional villages.
Cruise Details
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Wilsons Birds of Paradise
from $10,050
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Raja Ampat To the Volcanoes of Maluku

Sorong to Ternate - 12 Day Itinerary aboard Katharina
  • Snorkel Raja Ampat reefs
  • Spot birds of paradise
  • Visit Mioskon Island
  • Explore Waisai village
  • Discover Misool caves
  • Experience Maluku culture
Starts / Ends
Sorong / Ternate Island
Activities
Snorkeling, Kayaking, Small Ship Sailing, Wildlife Viewing, Village Visits, Archaeological Site Visits, Stand Up Paddle Boarding
Activity Level
Variable
Discover Indonesia on Katharina over 12 days from Sorong to Ternate. Snorkel vibrant reefs, spot birds of paradise, explore remote villages, and experience local culture in Raja Ampat and the Maluku Islands.
Cruise Details
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Grains and Spices at the market
from $10,050
EXPLORE

The Scents of the Spice Islands

Ambon to Ternate - 12 Day Itinerary aboard Ombak Putih
  • Visit Hitu Lama
  • Snorkel over black lava stream
  • View production of sago
  • Trek towards a forest waterfall
Starts / Ends
Ambon Island / Ternate Island
Activity Level
Variable
Make your way through the Spice Islands, a magical destination, on this 12-Day South Pacific cruise aboard Ombak Putih. Visit Hitu Lama, Gunung Api, Manipa, and Payahe Bay, to name a few of the marvelous stops on this luxurious cruise through paradise. You will have opportunities to snorkel and view local wildlife along the way.
Cruise Details
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Sunset over the town of Kuching, Sarawak, Malaysia
from $9,995
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An Equatorial adventure across North Borneo

Manila - Singapore - 17 Day Itinerary aboard Coral Geographer
  • Tour Culion Island history
  • Explore Puerto Princesa
  • Visit Sepilok Orangutans
  • Learn Marinduque traditions
  • Visit Brunei’s royal sites
Starts / Ends
Manila / Singapore
Activity Level
Variable
Sail from Manila to Singapore aboard Coral Geographer on this 17-day cruise. Visit remote islands in the Philippines, encounter orangutans in Borneo, tour historic cities, and discover diverse cultures. Swim in coral reefs, walk through mangrove forests, and explore vibrant markets and heritage towns.
Cruise Details
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Aerial view of Raja Ampat
from $12,195
EBD
EXPLORE

Idyllic Raja Ampat & Cenderawasih Bay

Roundtrip Denpasar - 10 Day Itinerary aboard Greg Mortimer
  • Explore Cenderawasih Bay
  • Immerse in West Papuan culture
  • Experience Pulau Num lagoons
  • Admire Raja Ampat reefs
  • Discover Wayag’s limestone cliffs
  • Birdwatch in Waigeo
Starts / Ends
Denpasar / Sorong
Activity Level
Variable
Uncover Indonesia’s Cenderawasih Bay and Raja Ampat on a 10-day cruise aboard the Greg Mortimer. After flying from Denpasar to Sorong, explore pristine islands, snorkel with whale sharks, dive in biodiverse waters, and experience local cultures, including visits to Wayag and Waigeo islands.
Cruise Details
0
Cruising Adventures! Komodo Dragon
from $12,700
EXPLORE

SeaTrek with Corals, Cultures & Dragons with Nicole, Coral Specialist

Bitung - Komodo - 16 Day Itinerary aboard Katharina
  • Snorkel vibrant Indonesian reefs
  • Meet Bajau sea gypsies
  • Swim with whale sharks
  • Track Komodo dragons Rinca
Starts / Ends
Bitung / Komodo Island
Activities
Whale Watching
Activity Level
Variable
Experience 16 days aboard Katharina from Bitung to Komodo: snorkel vibrant reefs at Punten, Ratatotok, and Malenge. Meet Bajau sea gypsies, explore Wakatobi, swim with stingless jellyfish, visit Bonerate’s traditional shipyards, encounter Komodo dragons, manta rays, and witness breathtaking sunsets at Gili Lawa Darat.
Cruise Details
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Forgotten Islands villagers performing a traditional dance in cultural attire.
from $29,790
EXPLORE

Raja Ampat, West Papua, & Forgotten Islands Expedition

Sorong to Labuan Bajo - 22 Day Itinerary aboard Aqua Blu
  • Dive Wayag’s Figure Eight Rock
  • Explore Banda Neira’s Dutch forts
  • Experience Melissa’s Garden
  • Observe Abui Tribe’s dance
  • Tour Fort Revenge on Pulau Ai
Starts / Ends
Sorong / Labuan Bajo
Activity Level
Variable
Embark on a 22-day cruise aboard Aqua Blu through Raja Ampat, West Papua, and the Forgotten Islands, starting in Sorong and sailing to Mioskon, Aljui Bay, Wayag, Penemu, and Banda Neira. Discover vibrant reefs, ancient forts, remote villages, and rich marine life from Pulau Koon to Alor, Maumere, and Labuan Bajo.
Cruise Details
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Beautiful wild coast of Raja Ampat, Indonesia
from $14,375
Save 15%
EXPLORE

Indonesian Explorer: Raja Ampat to Papua New Guinea

Bali - Port Moresby - 18 Day Itinerary aboard Heritage Adventurer
  • Visit Raja Ampat
  • Lookout for the endemic birds
  • Explore Komodo National Park
  • Swim at Triton Bay
Starts / Ends
Bali / Cairns
Activity Level
Variable
Aboard Heritage Adventurer on this 18-day expedition cruise to Indonesia's remote and little-known tropical islands, from Raja Ampat to Papua New Guinea, see whale sharks in Triton Bay, visit Komodo National Park, home to the famed Komodo Dragon, and more.
Cruise Details
0
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