Indonesian police have provided new details about how Australian authorities allegedly intercepted an asylum seeker boat, transferred the passengers onto two boats and sent them back to Indonesia.

One of the boats provided by Australia allegedly ran out of fuel during the journey and the asylum seekers had to climb onto the other boat which later crashed onto a reef.

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The documents, provided to the ABC by local police deputy chief commissioner Ronalzie Agus, detailed the journey of the asylum seekers from West Java to the waters off East Timor and back to Indonesia.

In their investigation into the turn-back operation and the allegations that Australia paid money to the crew, Indonesian police have interviewed six witnesses as well as the captain and crew of the boat.

Some of the passengers have also reported that an Australian Customs official paid money to the crew of the asylum seeker boat.

The police document about the initial findings of the investigation is in the form of a PowerPoint presentation and put the amount of money paid at more than $US30,000.

It detailed how the boat was allegedly intercepted by Australian authorities twice and taken to Australian waters before the 65 passengers and six crew were sent back to Indonesia.

En route they ran aground on a reef and had to be rescued by local villagers.

Indonesian police have also provided the ABC with photos of the thousands of dollars the crew were allegedly paid, as well as a stricken wooden boat provided by Australia in order to get the asylum seekers back to Indonesia.

Indonesia reacts angrily to claims of payments

The head of Indonesia's military (TNI), General Moeldoko, has reportedly described the tactic as unethical.

"That conduct was inappropriate. That's my view, but I would not give comment on the political context of a relation[ship] between two countries," he said.

General Moeldoko also defended Indonesia's ability to adequately patrol its vast waterways.

"Our sea border is so long — 81,000 kilometres — with our current military power, with its insufficient navy capabilities ... some sectors were sometimes missed," he was reported as saying.

The chairman of the country's parliamentary commission that covers foreign affairs, Commission One, told reporters at the national parliament that Indonesia and Australia needed to work together diplomatically.

Mahfudz Sidiq also hit out at the tactic of paying the boat crew as dishonourable.

"They bribed fishermen," he said.

"They knew exactly that our fishermen are needy and they bribed them. The conduct done by Australia toward Indonesian civilians ... was dishonour[able]."

Prime Minister Tony Abbott was asked about the reports by Opposition leader Bill Shorten in Question Time.

"We adhere to Australian law and we stop the boats. That is what we do," Mr Abbott said.

"We will do whatever is necessary, within the law and in accordance with our values as a decent and humane society, to stop the boats and to ensure that they stay stopped.

"Not only is what this Government has done legal, it is moral, it is absolutely moral because the most moral thing to do is to stop the boats and save the lives."

Chronology of the boat's journey

Some of the money allegedly given to a people smuggler. ( Indonesian Police )

The document provided to the ABC is in the form of an internal police slide presentation and said the five crew from Manado in North Sulawesi and one from Jakarta were recruited by people smugglers in early April.

The men were enlisted by someone identified by the initials AJ in Jakarta to work on a fishing boat with a promise of wages of about 150 million rupiah ($14,000).

On April 16 they gathered at Cempaka Hotel where they stayed for two nights before being bussed to Tegal on the north coast of Java.

They stayed at a hotel in Tegal while looking for a suitable boat. Once a boat was found, the crew travelled by sea to Cidaun beach on the south coast of West Java.

About 2:00am on May 5, the 65 asylum seekers began being delivered to the boat.

The passengers included 10 Bangladeshis, 54 Sri Lankans and one person from Myanmar. Among them were three children and four women, one of whom was pregnant.

A man identified as AY, who had also been involved with providing accommodation for the crew, told them that the 65 people should be taken to New Zealand.

Around 4:00am the boat departed towards New Zealand through the Java Sea. The police document said the boat passed Bali and continued further east past West Timor.

Crew warned by Australian Customs boat

Near East Timor the boat was allegedly crossing international waters when an Australian Customs ship stopped it.

Customs explained to them that their boat could not enter Australian waters and warning cards were distributed, saying: "Without a visa you cannot enter Australia."

After Customs gave a warning to the crew and the asylum seekers, they were released and continued towards Australian waters for about four days.

They were stopped again and detained by personnel from a Customs boat and Australian Navy ship, allegedly in international waters.

Then the captain, Yohanis Humiang, allegedly went to the Customs ship, was interrogated, and told the boat could not reach New Zealand because of the boat's condition and the waves.

The Indonesian police document alleges there was a deal between Australian Customs and Yohanis Humiang that the asylum seeker boat would be secured and escorted to Australian waters by Customs and the Navy — a trip that took four days.

When they arrived in the area they were registered and identified by the Customs officials.

After their details were taken, some of the asylum seekers asked to board to the Customs ship but some stayed on the boat captained by Yohanis Humiang.

The boat was then taken back towards Australia's Ashmore Reef and anchored there for two days

The crew of the boat and the rest of the asylum seekers then asked to go on board the Navy ship.

The Jasmine, which Indonesian police say was given to people smugglers by Australian authorities ( Indonesian police )

Two wooden boats belonging to Australia, called Jasmine and Kanak, were then provided and the group split in two, with 32 passengers transferred to one boat, 33 asylum seekers put on the other and three crew transferred to each boat.

They were given lifejackets, a map and directions to Rote Island. The ABC has previously reported that food and other supplies were also provided to those on board.

It was at this point that the captain was allegedly given as much as $US6,000 while the crew were given $US5,000 each, bringing the total paid to $US31,000.

The crew then took the asylum seekers towards Indonesian waters and Rote Island, a voyage that took about eight hours.

When they approached Rote Island, Jasmine ran out of fuel and Kanak had to take the passengers on board, meaning all 71 people were on board the one boat.

Indonesian police were told some asylum seekers then started getting angry, began fighting with each other and also threatened the crew because they wanted to go to New Zealand.

The Kanak eventually crashed onto a reef at Landu Island. ( Indonesian Police )

About 5:00pm on May 31, Kanak crashed onto a reef at Landu Island, near Rote Island, which is off West Timor.

Some people jumped from the boat and made it to the nearest village. Locals then helped to evacuate the rest of the asylum seekers from the stricken boat.

The document said the boat crew hired a small canoe to take themselves to land, understood to be Rote Island.

One of the villagers called local police, telling them that an asylum seeker boat had crashed on Landu Island.

The southwest Rote police chief went to Landu Island to "secure" the asylum seekers and search for the crew.

According to the locals, cited by the document, the crew fled to Rote Island but around 9:00pm police arrested the six crew members.

They remain in custody and could each face a maximum of 15 years in jail and up to 1.5 billion rupiah ($145,000) in fines.

Immigration authorities are holding the 65 asylum seekers at a hotel in Kupang, West Timor.