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.

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.

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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.

Immigration Minister Peter Dutton has backtracked on initial denials that people smugglers were paid to turn their boat around. Photo: AAP

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 $30,000.

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.

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.

Crew warned by Australian Customs boat

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

The Jasmine, which Indonesian police say was given to people smugglers by Australian authorities before running aground on a reef.

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.

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.

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 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.

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

– ABC