A Salvation Army risk and compliance officer, who is only identified as "Andrew", wrote to a Tamil man on the charity's letterhead in January 2014 saying: "You can expect to remain in this facility for a very long time whilst this process is undertaken.

"You may be given an opportunity to be re-settled in PNG but I am not sure when or if this may occur. The only other option available to you is to seek repatriation with the assistance to IOM (International Organization for Migration) to your country of origin.

"If you choose not to go home you will spend a very, very long time here. You have been told lies by people smugglers."

The Salvation Army has declared publicly its opposition to offshore detention and received more than $70 million under a contract to provide humanitarian services on Manus Island and Nauru between 2012 and 2014. A spokesman acknowledged the letter was written by one of its staff "in consultation" with the Immigration Department.

He said the group's contract with the department required it to communicate official information to detainees, including the time frames associated with the processing of their asylum seeker claims.

The message could have been communicated more sensitively, the spokesman said, but it accurately reflected the government's July 2013 policy decision not to re-settle boat arrivals in Australia.

"The Salvation Army agrees that the content of the letter, read in isolation, is incredibly harsh, however, there was no malicious or cruel intent held when this letter was written," the spokesman said.

An Immigration department spokeswoman said the contract with the Salvation Army contained no requirement for the Department to "vet, oversee or help draft" correspondence to transferees.

The Tamil man was part of a group known as "OPK" which attempted to enter Australia by boat in mid-2013.

"Perhaps in some part, the content of the letter reflected a choice between two incredibly difficult situations, firstly, where transferees would be left in limbo - not knowing what would happen to them or still hoping that they would be resettled in Australia - or alternatively, communicating the incredibly difficult message that post 19 July 2013, transferees would not be resettled in Australia and according to the government policy there would be absolutely no exceptions," the Salvation Army spokesman said.

"In communicating the latter, it was hoped that this could at least give the transferees some certainty about their future and some choice (although a very bleak choice) as to whether they would remain at the centres or return to their country of origin if they preferred to do so."

Asylum seekers have also alleged that they were beaten by private security guards during an operation to end a January 2015 Manus Island hunger strike, and have told Fairfax Media in a series of letters that they were jailed in the nearby Lorengau police cells for up to 21 days.

Leaked files from Broadspectrum, the company contracted to run the Manus Island and Nauru centres, support some of the claims of injury and placement in the police cells.

The company's files show detainees sought medical treatment after complaining of nerve pain in their arms, which they claimed was the a result of having their wrists tightly bound by plastic restraints during the hunger strike.

One detainee wrote in a letter that he was kicked in the head by security guards while he was in the Lorengau police cells and was left shirtless during his 21 day stint in the cells. Another said the cells were filthy and that "the toilet sewage would come to where we slept".

An Iraqi asylum seeker has claimed in a letter that he was beaten about the head with a stick by security staff, resulting in damage to his eyesight and the loss of teeth.

The letters do not specify whether the security staff who committed the alleged assaults were Australians or local PNG employees.

The leaked Broadspectrum files show that many complaints against security staff are found to be unsubstantiated due to a lack of evidence.

The files show that another detainee complained of being beaten in the chest, abdomen and face during the January 2015 hunger strike before being handcuffed and thrown into a vehicle.

His alleged beating took place despite some security staff trying to advocate on his behalf that he had not been causing trouble.

An official complaint about the man's case lodged in July by the International Committee of the Red Cross last year reveals he was then jailed in the Lorengau police cells for up to 17 days before he received any medical treatment.

At the time of the operation to end the hunger strike, Immigration Minister Peter Dutton denied excessive force had been used but admitted a degree of force had been necessary.

Some asylum seekers say they suffer on-going health issues as a result of their treatment.