The Indonesian navy last week captured a fishing boat smuggling one tonne of crystal methamphetamine in 41 rice sacks, off the waters of Batam island.

The smugglers, using the boat Sunrise Glory, were first spotted by navy patrol KRI Sigurot 864 on Wednesday afternoon as it entered Indonesian waters along the Singapore Strait.

Yesterday, Deputy Navy Chief Achmad Taufiqoerrochman said the navy was acting on a tip-off from Indonesia's National Narcotics Agency (BNN), which has been tracking the suspects since December.

The Sunrise Glory was stopped and boarded by navy personnel for inspection in the Phillip Channel near islands off Batam.

While the boat was flying a Singapore flag at the time, its crew was able to produce only photocopied registration documents purportedly from Indonesia and there were also signs that it had used the name Sun De Man 66.

A Taiwanese flag was also discovered on board, and the crew of four Taiwanese are now being held and investigated for operating the boat under various false flags for illegal fishing or drug smuggling.

Indonesian Custom officers, with help from sniffer dogs, later found the drugs on board the fishing boat during further examination at Batu Ampar Port in Batam and detained the crew for investigation.

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Vice-Admiral Achmad said preliminary investigations indicate that the drugs, which were hidden in 41 rice sacks in the lower deck of the boat, was headed for Taiwan waters, and subsequently to Australia.

"But it is still early. We will submit this investigation to the BNN for the next process," he added.

The case comes after Indonesian police and Customs officers intercepted a 66kg shipment of the same type of drugs, better known by its street name crystal meth, shabu-shabu or Ice, just last month.

The Riau Islands' police chief, Inspector-General Didid Widiadi, said then that the drugs were being shipped from Singapore to Batam by sea and would later be flown to Jakarta by air.

Indonesia already has some of the world's toughest drug laws and remains one of 33 countries that use capital punishment for drug-related offences.

But the country has struggled to contain the drug problem, with officials estimating that there are at least 1.2 million drug abusers in the country, which has a population of more than 250 million.

Ecstasy, heroin, marijuana and methamphetamine are the drugs of choice for substance abusers in Indonesia, similar to the trend in many other countries in the region.

According to Police Inspector-General Arman Depari from the BNN, almost 80 per cent of narcotics are smuggled by sea and the Sunrise Glory is suspected to be a vessel used by a Taiwanese syndicate to supply dealers in Asia.

Tougher action taken by countries such as China and the Philippines in the war on drugs has led to traffickers sending their supply to Indonesia, he added.

President Joko Widodo has warned that the drug situation has put the country in a national emergency. Last July, he issued a shoot-to-kill order against drug dealers, especially foreign traffickers, who resist arrest.

The move, which mirrored that of President Rodrigo Duterte in the Philippines, was criticised by human rights groups such as Amnesty International, which said that a total of 55 Indonesians and foreigners were shot and killed without judicial process as of August last year.