The waters of the 5000km-long archipelago nation are the most dangerous on Earth, according to the UK-based International Maritime Bureau (IMB), which tracks incidents of piracy and attacks on shipping.
The IMB, a branch of the International Chamber of Commerce, reported 121 of the 445 attacks on commercial shipping in 2003 occurred in Indonesian waters, a 20% increase over the previous year.
Twenty-one seamen died, more than 350 were taken hostage and 70 remain missing.
"The Indonesian navy has been in a decrepit state for quite some time now. They are not able to adequately patrol and protect their waterways, in particular the Malacca Strait," says Dr Andrew Tan of the Singapore-based Institute for Defence and Strategic Studies.
The strategically important strait, which is the focus of much of the piracy, separates the Indonesian island of Sumatra from the Malaysian peninsula and Singapore, and links the Indian Ocean and the South China Sea.
Nine hundred ships a week carrying roughly one-quarter of the world’s trade and oil run the gauntlet of pirates as they pass through the strait.
Stirred into the mix are Singapore's concerns about terrorists plowing a hijacked tanker into the nation-state’s port, the world’s busiest hub.
Singapore fears that a tanker
might be rammed into its port
"They've certainly been talking a terrorist strike up a lot, holding all sorts of conference and inviting experts to come from around the world," says Tan.
So serious has the problem become that a senior American naval officer earlier this month publicly disclosed plans for the deployment of US marines and special forces troops in the region.
"We're looking at putting special operations forces and marines on high-speed vessels so that we can use boats that might be incorporated with these vessels to conduct effective interdiction," said Admiral Thomas Fargo, the US military commander responsible for the Asia-Pacific region. "There is widespread support for this initiative."
Officials in both Indonesia and Malaysia reacted angrily to the suggestion of a permanent American military presence in the strait and the US has subsequently "clarified" the admiral’s comments.
The smouldering Superferry 14
in Mariveles Bataan
"The incidents of piracy have increased but they do not warrant the sending in of a US marine force to actually police the area: that’s not on and the Americans know it," says Indonesian Foreign Ministry spokesman Marty Natalegawa.
"We are the first to admit there's great room for improvement but we also need to dispel the notion that there's anarchy in the Straits of Malacca; that anything goes."
Indonesia's top admiral told journalists last week the matter had not been discussed during February meetings with Fargo in Jakarta.
Details of recent attacks in Indonesian waters read like an 18th century naval logbook, full of fierce Bugis pirates with knives between their teeth shimmying up anchor chains in the middle of the night.
And while the tools of the pirating trade have changed, their modus operandi remains pretty much the same.
The most common practice is for pirates to take advantage of lax security to board vessels, rough up the crew, loot the stores and flee into the night.
They sometimes ransom the crews back to their owners. In other cases, ships and their cargoes have vanished for years only to resurface, newly painted and renamed, plying routes in southern China and India, their crews never heard from again.
In a three-day period at the end of March, the IMB reported four attempts were made to board tankers in the Malacca Straits by boats loaded with men carrying AK-47s.
The boarding parties were repulsed when the vessels under attack displayed "crew alertness", sounding horns and sweeping the area with searchlights.
An alert watch also detected two men climbing the anchor chain of a tanker berthed in Balikpapan, Kalimantan, and drove off the pirates.
Four crew members of the tanker Cherry 201 were not so lucky. Pirates murdered the Indonesian sailors in February after the vessel’s owner reneged on an agreed-upon $8500 ransom.
"Risk and potential targets used to be assessed on the basis of the intrinsic value of cargoes. The main focus now has to be the strategic intentions of terrorist groups"
Captain Pottengal Mukudan,
International Maritime Bureau
The IMB, which could not be reached for comment, acknowledged the dangerous potential of a link-up between loosely organised bands of pirates and international groups.
"The essential nature of the threat has changed," IMB director Captain Pottengal Mukudan told the South China Morning Post in November.
"Risk and potential targets used to be assessed on the basis of the intrinsic value of cargoes and the ships carrying them. That no longer applies. The main focus now has to be the strategic intentions of terrorist groups.
Those responsible for the security of ports and ships have to put themselves in the minds of terrorists and ask: 'How attractive a target do we present in terms of terrorist objectives?'"
The bombing assault on the USS Cole in Yemen in 2000, and the copycat attack on a French tanker two years later drove home to the Singaporean government its vulnerability, says Tan.
Then in 2002, Singaporean intelligence broke up a "terrorist cell" they claimed was affiliated to al-Qaida, and uncovered plans to use small, explosives-laden boats to attack US naval vessels berthed there.
The damaged destroyer USS Cole
"There were several scenarios including hijacking and sinking a ship in the Malacca Straits, or crashing a hijacked chemical tanker into the Singapore port. That would bring trade to a halt throughout southeast Asia, not to mention the number of casualties it would cause," says Tan.
"The Singaporean authorities are confident they can prevent this from happening given the extensive measures that have been taken to prevent those hijackings."
Singaporean naval ships now escort ships containing chemicals out of port, and they have developed security countermeasures including commando boarding parties and ship-to-ship interdictions, said Tan.
And the Singaporean navy and Japanese coast guard have conducted numerous training exercises. The Japanese receive 80% of their oil via the Malacca Strait.
Once they reach Indonesian territorial waters however, they are on their own.
"We are not being naive here, we are aware of the threats and these types of scenarios, about ships being commandeered by terrorists. This fear is not exclusively Singapore's," says Natalegawa.
"This issue also supports Indonesia's view that countries in the region need to discuss these security issues among themselves and come up with a regional strategy.
"In the absence of discussions what we have is this constant mischievous idea-dropping from outside the region and the countries scrambling for a response."