Peter Slipper's former staff member James Ashby has announced plans to file his sexual harassment case against his former boss with Fair Work Australia, despite it being thrown out of the Federal Court as an "abuse of process".

The court ordered Mr Ashby pay Mr Slipper's legal fees, declaring the case had been politically motivated to damage the former parliamentary speaker and advance the interests of the Liberal National Party (LNP).

Mr Ashby's spokesman, Anthony McClellan, says an appeal will be lodged against that decision in mid-January, and has today indicated his client will also pursue other legal avenues as well.

"Later today, we are planning to file James Ashby's sexual harassment case with Fair Work Australia, with the aim that the whole evidence and that the witnesses can be tested in open court at the appropriate time," Mr McClellan told reporters outside court today.

"This is designed to preserve and protect James' legal rights. In that matter, Harmers Workplace Lawyers will continue to act for Mr James [sic]."

He refused to answer journalists' questions, saying: "We can't make any further comments at the moment".

Lawyers for Mr Ashby appeared in court this morning as part of a costs application brought on by Mr Slipper.

The Federal MP is seeking a court order that would require Mr Ashby pay costs "on an indemnity basis", meaning that the full expense of defending himself would be recoverable, instead of the usual level of between 50 and 70 per cent.

Mr Slipper has taken the unusual move of lodging a similar application against Mr Ashby's legal team, Harmers Workplace Lawyers.

A hearing on the matter has been adjourned until February next year.

When Justice Steven Rares handed down his judgement last week, he was scathing of Michael Harmer of Harmers Workplace Lawyers, describing his decision to include "scandalous and irrelevant" references in his original application as "an abuse of Mr Harmer's professional obligations to the court as a lawyer".

Following the judgement, Mr Harmer said he was "shocked and disappointed" by the court's decision, and indicated that he would argue strongly on appeal that: "the conclusions in his Honour’s judgment made about our conduct of the case are simply not justified by the evidence".

In a statement issued after the court handed down its judgement, Mr Slipper said he felt vindicated by the outcome and thanked his family and friends for their support during an "extraordinarily difficult" time.