Cruise Indonesia

14 Cruises
7 Offers
Cruise far beyond the reach of what most travelers see in Indonesia. On our active itineraries, you’ll encounter rare wildlife and welcoming locals as you explore isolated coastlines, reefs and islets. Let’s get started.
Trips, Tours & Cruises

Authentic, Active Indonesia Cruises

View All Indonesia Cruises
14 Cruises
7 Offers

Our Indonesia small ship cruises include a range of itineraries from classic Bali cruises to farther-flung routes. Experience Raja Ampat’s famed underwater world scuba diving or snorkeling alongside skilled naturalist guides. Tap into the the history and markets of the Spice Islands. Island hop around Komodo National Park to see the world’s largest lizard…

Our Indonesia cruises epitomize small, sustainable travel in the region, with a focus on wildlife and local culture. Our team is here to assist you one-on-one to select and book your trip. Browse our well-rounded Indonesia cruise selection and let us help you sort through the options to ensure you get on the best itinerary for your interests.

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Cruise Indonesia
with AdventureSmith

AdventureSmith’s cruises let you experience Indonesia’s wide expanse of islands in an active, efficient way. From the Spice Islands to Bali, let our experienced team guide you through the wide array of small ship itineraries. Why choose to cruise Indonesia with us?

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Work with one dedicated U.S.-based specialist to purchase & prepare for your Indonesia cruise.

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We can match you with trusted Indonesia small cruise ships, all intimate at under 120 guests.

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Our relationships & on-the-ground travels result in tried & trusted, reputable cruises.

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Our Indonesia cruises include guided snorkeling, scuba diving, hiking & skiff rides.

A two-masted Indonesia sailing ship sits at anchor in bright blue water with green tree leaves in the foreground

The Lay of the Land

At nearly 750,000 square miles, Indonesia is the world’s largest island country and the seventh largest by combined sea-and-land area.

Unless you have unlimited time, you simply cannot sail/see it all in one cruise itinerary. Thus, understanding the regions and knowing what you want out of your travel experience and ship are paramount.

Cruising Indonesia for Wildlife

While wildlife encounters can never be guaranteed, seeking out endemic creatures is half the fun. In Indonesia, you can set your sights on Komodo dragons, birds-of-paradise, whale sharks and manta rays, among other exciting animals, but there are geographical nuances to consider.

Komodo and Rinca Islands are the islands to visit if you are keen to see Komodo dragons. Snorkeling near Flores Island will offer you the best chance to see manta rays and sea turtles in deep currents, and some Raja Ampat routes hone in on the best chances to spot birds-of-paradise. Learn more in our guide to the regions below.

A close up of a komodo dragon's head and two arms with its forked tongue sticking out

“Our Indonesia small ship cruises focus on activity, wildlife & exploring remote islands.”

Lesser Sunda Islands: Flores, Komodo & Bali Cruises

The most popular cruise itineraries are located in the Lesser Sunda Islands, perhaps due to the international airport on Bali and the island being a household name in travel thanks to its many established resorts. From west to east, the Lesser Sunda Islands comprise Bali, Lombok, Sumbawa, Flores, Sumba, Timor, the Alor archipelago, the Barat Daya Islands and the Tanimbar Islands, with the most common expedition cruise routes sailing regularly between Bali and Flores.

Each of these islands are different in their own right with myriad earthy highlights including volcanoes, rainforests, waterfalls, mangroves, white-sand beaches and even savannah. This diverse landscape also holds a variety of wildlife that includes Komodo dragons (Rinca & Komodo Islands) and manta rays in the deep channels that separate the Indian Ocean from the Pacific. Traditional lifestyles, quiet coastal villages, tribal rituals and intriguing ancestral traditions are also a major draw for travelers to the Lesser Sundas.

A man in boardshorts and no shirt stands on a hilltop above a small sandy beach peninsula with no one on it and a small ship and volcanoes in the water below

Raja Ampat Cruises

For travelers looking for an immersive experience into the natural world of Indonesia, a cruise through the archipelago of Raja Ampat is the ideal modality. Located right in the heart of the Coral Triangle, this biodiverse area contains 450 species of reef-building coral, 1,400 species of fish and intriguing endemic sea life—the stingless jellyfish of the brackish interior lakes being the perfect example.

This kaleidoscopic underworld is ideal for the avid diver or snorkeler and pairs nicely with the stunning karst islands and unique bird life, including striking birds-of-paradise. The island biogeography of these birds helped Alfred Russel Wallace formulate his theories of speciation, much like the finches of the Galapagos did for Charles Darwin.

Additionally, voyages in Raja Ampat offer adventures hiking, exploring caves and inner-island jungle walks to stunning waterfalls.

A small ship anchored in turquoise waters among several islands in Indonesia.

New Guinea Cruises (West Papua & Papua New Guinea)

While West Papua is technically the only territory of Indonesia, the island of New Guinea is often an itinerary stop or embarkation point for many Indonesia cruises. Many Raja Ampat cruises begin their journey in West Papua out of Sorong.

Like its neighbor Raja Ampat, New Guinea is a hotspot for birds-of-paradise, but even more so as all but two genera are found here. At their core though, trips to New Guinea are truly cultural, offering a look into a world that very few outsiders see.

West Papua and Papua New Guinea cruises highlight remote villages, traditional art and authentic rituals providing human connection with peoples that are living a very similar life to their grandparents, quite the feat for the twenty-first century. Papua New Guinea is also home to stimulating World War II history and is dotted with historic places of interest, monuments and tributes honoring the fallen. The colorful biodiversity of the underwater world delivers the perfect balance to days filled with culture and history.

Local village children dressed in tribal wear in Indonesia.
Photo by AdventureSmith Specialist Andrew Browning

Spice Islands Cruises

Indonesian Spice Islands cruises offer a unique historic experience and deep cultural interactions among beautiful islands. The Spice Islands were mapped on ancient trade routes long before the Europeans even began searching out the Islands’ nutmeg, cloves, mace and pepper. The Portuguese, the first Europeans to start trading spices on a large scale from the Spice Islands in 1598, cornered the market for almost 80 years, infusing the area with Portuguese culture.

The clashes between the varying nations and cultures in the region for centuries offers a fascinating historic journey that can capture any traveler’s imagination. Remnants of this highly utilized trade route are still seen today on Spice Island cruise itineraries that also can include snorkeling with whale sharks; exploring lush national parks; visits to traditional villages, colonial forts and palaces; and ideal snorkeling, diving and underwater adventures.

Various local spices set out in bowls at a market in Indonesia.

Sulawesi Cruises & Kalimantan (Borneo)

Sulawesi, the Indonesian island east of Kalimantan (Borneo) and west of Raja Ampat, is perhaps the most unknown gem of the country’s many islands. Its shorelines and atolls are freckled with human settlements that rarely see tourism, so this is a land of true adventure travel and modern cultural experiences. Villages here are authentic working/living places for a variety of locals who make their living farming and fishing. This includes the nomadic Bajau people, commonly called the sea gypsies.

The unique shape of the island into several long peninsulas offers coral reefs alongside varied coastal geography ranging from steep mountains to palm-lined beaches. The Togean Islands offer chances to swim with stingless jellyfish, and keen eyes should look for tarsiers and macaques. Sulawesi is also home to the Bugis, Indonesia’s famed shipbuilders, so your itinerary may include seeing giant wooden vessels being built on the beach.

If orangutans are on your bucket list, be sure to look for Sulawesi cruise itineraries that include stops in Borneo. Several of our trips include stops or pre-cruise trip extensions here.

A Note About the Wallace Line

Indonesia is famous for the Wallace Line, a faunal boundary separating two eco-zones (Asia and Wallacea, the transitional zone between Asia and Australia). The “line” was drawn by naturalist Alfred Russel Wallace in 1859 and runs between Borneo and Sulawesi down to the strait between Bali and Lombok. Traveling around this line is a thrill for naturalists as it’s one of the most distinctive biogeographic areas on Earth. West of the line you will find larger terrestrial mammals (tigers, elephants, orangutans), and east of the line look for marsupials, Australian cockatoos and birds-of-paradise. The Indonesian island of Sulawesi is an interesting exception to the Wallace Line with black macaques, pigs and tarsiers.

Java & Sumatra Cruises

Most itineraries explore Indonesia from points north and east of Bali. However, select itineraries will cruise along the western Indonesian islands of Java and Sumatra, linking up with Singapore. While Java is home to a majority of the Indonesian population, small ship cruises here will opt to mostly visit uninhabited offshore isles and small villages. In this region travelers can explore unspoiled coral reefs, deserted black- and white-sand beaches, lush jungle and child volcanoes of the famous Krakatoa.

The Places in Between: “Positioning” Indonesia Cruises

A fun way to see Indonesia is to “position,” or cruise with the boat as it sails between these iconic regions. These trips are often longer in length and include more days at sea (sailing vs. venturing off the ship) but connect you to the unseen places of Indonesia and allow you to relax with the rhythm of the ocean. Positioning cruises are also excellent choices to add on to a voyage. For example, a three-week positioning itinerary could be to sail south from Sulawesi to Flores, then stay on the ship all the way west to Bali!


See all the expedition cruise options in Indonesia.


Cruise Indonesia

Temperature & Rainfall

Month Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
Avg. High (F) 88 88 88 88 88 88 84 84 86 88 88 88
Avg. Low (F) 73 73 73 73 73 72 72 72 72 73 73 73
Avg. Water Temp (F) 84 84 84 84 84 82 81 81 81 82 84 84
Avg. Rainfall (Inches) 13.8 11 20 12 8 7 4 3 3 6 10 16

Year-Round Indonesia Cruising

Indonesia cruises are available every month of the year, but ships often follow the trade winds and weather patterns to sail certain locations during their drier, less-windy months. If you are seeking to visit Raja Ampat, for example, plan your trip in the winter months (roughly, October through February). If your course is set on a Bali cruise, you can look for most sailings running from March through September. Climate data listed above is from Denpasar, Bali.

Seeking More Details about Weather, Regions & Wildlife?

Cruise Indonesia

AdventureSmith's Director of Sales & Operations reviews his Raja Ampat cruise aboard the 24-guest Ombak Putih. Follow his adventures swimming with stingless jellyfish and seeking out the famed bird-of-paradise.
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AdventureSmith sails Indonesia's most remote reaches, along the eastern coast of Sulawesi. Learn our insights on this trip and the highlights of a Sulawesi cruise.
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Learn about the food, cabins, crew and more from AdventureSmith experts who've been aboard these unique Indonesian sailing vessels.
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An AdventureSmith cruise expert goes aboard in Australia to write this ship review of the 120-guest Coral Adventurer. Read about her favorite features and cabin insights.
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An intimate look at island hopping in Indonesia between Bali and Flores. Learn why this trip is the perfect fit for AdventureSmith's style of cruising.
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