A federal public servant sacked for making false bullying allegations against his boss could also face criminal action for claiming workers' compensation for mental stress caused by the "harassment".

The former Environment Department worker was sacked this year after he and his colleagues plotted to "play the indigenous card" to get their boss sacked.

The Fair Work Commission, which this week threw out John Hunter's unfair dismissal claim against the department, noted that one of the allegations against the former Level 1 executive could end up in a criminal prosecution.

Mr Hunter was sacked for committing multiple breaches of the Australian Public Service code of conduct as part of his "vexatious" and "deceptive" pursuit of his boss, Neil Bensley, at their North Queensland work unit last year.

One of the alleged breaches, that of Mr Hunter "providing false and misleading information to the department and to (federal workplace insurer) Comcare", is now the subject of a separate legal battle in the Administrative Appeals Tribunal.

The tribunal's Brisbane office confirmed on Friday that the former public servant was challenging Comcare's decision in the matter, but a confidentiality order on the case meant that no further information could be released. The unfair dismissal decision could have repercussions across the public sector, which is faced with a spiralling bill for workers' compensation claims for psychological injuries, many of them related to accusations of workplace bullying.

Fair Work commissioner Paula Spencer, who dismissed Mr Hunter's claim, did not make a finding on the allegation of providing false and misleading information, noting the matter was before the tribunal.

"This matter, as related to the Comcare application, is still the subject of proceedings and … the assessment requires consideration of different legislative tests in a different jurisdiction and could give rise to criminal liability," Ms Spencer wrote.

The commissioner also noted that she did not need to make a finding on the alleged deception, because the Environment Department had other reasons to sack its employee.

"It is also unnecessary to making a finding in relation to this reason, given the findings made in relation to the other reasons for dismissal, that justify the dismissal,'' Ms Spencer wrote.

More than 150 allegations of fraud were made against workers or healthcare providers in the Comcare scheme in the past financial year, with three of those cases now being pursued by federal prosecutors.