Prime Minister Julia Gillard says the inquiry into Federal Labor MP Craig Thomson is almost over.

Fairfax newspapers are reporting that Fair Work Australia (FWA) has finished its investigation into Mr Thomson, who is facing allegations he misused a union credit while he was the Health Services Union's (HSU) national secretary.

Two other HSU officials were also under investigation for other matters.

Mr Thomson, the union's president Michael Williamson and national secretary Kathy Jackson were told last month that FWA intended to make adverse findings against them, Fairfax reports.

They have been given several weeks to respond to the allegations and the workplace regulator will release its final report after considering their responses.

Mr Williamson said the allegations were "bread and butter stuff", while Mr Thomson said the newspaper had an "unreliable source".

FWA has been looking at allegations involving the union officials since April 2009, but a formal investigation did not start until March 2010.

Opposition Leader Tony Abbott says the length of time it has taken to investigate the matter is "scandalous" and it should be concluded as soon as possible.

"But this is not just an issue for Fair Work Australia," he said, adding it was an issue for the Prime Minister.

"In the light of today's reports I call on the Prime Minister to stand up before the cameras and declare whether or not she still has full confidence in Craig Thomson."

The minority government depends on Mr Thomson's vote in Parliament to survive.

Ms Gillard says the Government is not involved in the investigation.

"Fair Work Australia works independently from Government, anything about the investigations that you refer to I only know from today's newspapers, they're independent of us, the investigation is in progress and it should conclude," he said.

Ms Jackson said any allegations against her were without foundation and she was not aware she was being investigated.

ABC/wires