In a strongly worded decision handed down last month, Administrative Appeals Tribunal deputy president Gary Humphries said Comcare had used "unethical tactics" against former refugee Charles Koker, employed by the territory's Community Services Directorate at the Bimberi Youth Detention Centre.

Comcare disputed the criticism on Tuesday and said it would not seek repayment in the case.

Mr Koker was injured while attempting to restrain a young person at Bimberi in June 2013 and was in the process of completing a return to work program when he was told by his bosses to stay home after an incident involving his supervisor two years later.

The tribunal was told the youth worker reported feeling harassed after being asked by multiple unit managers and team leaders for medical certificates related to his absences from work in May 2015.

Medical certificates said Mr Koker should not have direct or indirect contact with his supervisor, and he was instructed to stay home and to "rest up" due to a lack of other suitable duties for him to perform.

He told the tribunal he would have accepted any offer of work made to him by his employer. Doctors cleared him to work normal hours in administrative duties in October 2015.

That month he submitted a claim for workers compensation related to anxiety and depression which he said he first noticed and sought treatment for as a result of "poor behaviour and abused behaviour" by a supervisor at work in May 2015.

Mr Koker told the tribunal he sought to return to work over a period of about seven months but was always told to remain at home.

Comcare issued determinations that Mr Koker was entitled to incapacity payments in 2015, but reconsidered the case and in April 2016 decided he was entitled to $24,949 less than he had been paid.

Mr Humphries, the former ACT senator and chief minister, said attempts to recover more than $10,000 he had been led to believe he was entitled to was "unconscionable".

He said Mr Koker had been effectively directed to stay home from work for most of nine months, despite being capable of engaging in suitable work.

"Mr Koker has relied on Comcare's implicit representations - that he was entitled to incapacity payments while he was directed to remain away from work - to his significant financial detriment.

"Had he been told early in this period that he was not entitled to this support, he would have had the option of quitting his position and seeking employment elsewhere.

"But he was not told this, and he now incurs a substantial debt which was entirely avoidable had Comcare dealt with him fairly."

Mr Humphries required Comcare to pay Mr Koker's costs for the case.

"Comcare is to be commended for the efforts it has made in recent years to reduce the premiums paid by its employer clients," he said in the decision.

"If its efforts to reduce costs extend to unethical tactics such as those employed against Mr Koker in this case, however, this effort must be regarded as much less commendable than it might first have seemed."

A Comcare spokesman said the insurer had not acted unfairly or unethically.

"Comcare has not and will not pursue a debt from the employee in this case," the spokesman said.

"This was an incorrect assumption by the deputy president, based on a document presented at the hearing that indicated debt recovery was a possibility.

"Comcare has written to the Administrative Appeals Tribunal President to take issue with the comments made in this decision. The Tribunal found Comcare's decision in this case to be correct, and there was no evidence of unethical behaviour."

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