Amnesty International has urged Australia to immediately stop its $300,000 military assistance program with Myanmar and help build a case for international prosecution against soldiers responsible for crimes against humanity.

Key points: Amnesty is calling for the immediate suspension of Australia's military training program with Myanmar

Amnesty is calling for the immediate suspension of Australia's military training program with Myanmar They say top military leaders ordered torturing of suspected Rohingya militants

They say top military leaders ordered torturing of suspected Rohingya militants Amnesty said Rohingya militants have also committed abuses during the fighting

Amnesty has released a report naming 13 senior military officers it believes are most responsible for human rights abuses against Rohingya Muslims in Myanmar's Rakhine State.

A coordinated campaign of killing, rape and arson caused more than 700,000 Rohingyas to flee to Bangladesh, where they are now enduring the monsoon in sprawling makeshift camps.

"We want to send a message to the Myanmar security forces — we know who you are," said Amnesty's Myanmar researcher Laura Haigh.

"This was not a series of rogue soldiers or rogue units, this was a tightly controlled operation that targeted the Rohingya just on the basis of who they were."

Amnesty said it based its findings on more than 400 interviews, mostly with survivors or direct witnesses of attacks, as well as forensic medical examinations and satellite imagery.

The human rights group believes there are numerous individuals within Myanmar's security forces who should face judicial proceedings for crimes against humanity.

The International Criminal Court is currently considering whether it has jurisdiction to mount such a case.

"What we'd like to see Australia do as a member of the human rights council would be to work towards the establishment of an accountability mechanism, something that would help collect and preserve evidence of the military's crimes to the level that would be accepted in a court," said Ms Haigh.

In the meantime, Amnesty said Australia should stop training the Myanmar military.

"We would want to see the immediate suspension of all military cooperation and assistance with the Myanmar security forces," said Ms Haigh.

Australian and Myanmar officials pose for an official photograph in Naypyidaw, Myanmar. ( Supplied: MNA )

Waterboarding, beard-burning

At the very top of Amnesty's list is Senior General Min Aung Hlaing, the commander-in-chief of Myanmar's military.

"He oversaw the operations, he actually went to northern Rakhine State himself in late September," said Ms Haigh.

"He's one of the individuals that we believe has command responsibility for crimes against humanity in Myanmar."

Senior General Min Aung Hlaing is the commander-in-chief of Myanmar's military. ( AP: Lynn Bo Bo/Pool )

Another senior figure named is Brigadier General Thura San Lwin, commander of the para-military Border Guard Police, which is accused of detaining and torturing suspected Rohingya militants.

"The torture they inflicted on men and boys was horrific — these are beating, burnings, sometimes burning of beards, waterboarding in some cases as well as sexual violence," said Ms Haigh.

Two other key figures named were the commanders of military units with reputations for human rights abuses that were deployed to Rakhine State in the weeks leading up to the so-called "clearance operations".

Major Aung Aung was the commander of the 33rd light infantry division, while Brigadier General Than Oo led the 99th light infantry division.

This week the European Union announced sanctions against seven military officials.

The Myanmar military and civilian government has previously denied almost all the allegations, saying the violence was a justified response to a terrorist threat from Rohingya militants.

Requests for comment sent to the Myanmar Government — from Amnesty and the ABC — went unanswered.

The Rohingya are one of the world's most persecuted peoples, and hold no civil rights in Myanmar. ( AP: Bernat Armangue )

Rohingya militants also committed abuses

Amnesty also accused Rohingya militants of grave human rights abuses.

On August 25, fighters from the Arakan Rohingya Salvation Army (ARSA) attacked police posts, which sparked the crackdown by Myanmar security forces.

Amnesty said ARSA murdered and abducted Rohingyas thought to be informants, burned two villages and massacred 54 Hindus in a single attack.

"Any international investigation must also look at these abuses," said the Amnesty report.