Concerns about possible misconduct within Tasmania's multi-million-dollar fox eradication program should have been investigated two years ago when they were raised with the Federal Government, according to federal independent MP Andrew Wilkie.

The ABC has obtained a report, written by a member of the eradication program, which questioned the veracity of evidence used to show fox activity in the state.

"Sufficient evidence exists to suspect that some hoaxing has occurred via mainland fox scats (faeces) being placed in the landscape," zoologist and report author Simon Fearn wrote in 2011.

Contamination through the mishandling of scats was possible, but "a determined hoaxer, particularly on staff, would be very difficult to nullify", he said.

"I don't know if there are foxes in Tasmania or not. I don't know if there's been misconduct in the taskforce or not, but I tell you what, there is so much evidence on the table now I suspect we've got a real problem," Mr Wilkie said.

Sorry, this video has expired Concerns about evidence used to justify fox hunts were raised in 2011

The Tasmanian politician has revealed that he met then-federal environment minister Greg Hunt in June 2014 to raise concerns about the eradication program.

Successive Tasmanian and federal governments have spent $50 million since 2001 on measures to stop the European red fox gaining a foothold on the island — the only Australian state thought not to have an established fox population.

"I expressed a number of concerns with Greg Hunt, firstly that there were allegations of misconduct within the taskforce by some taskforce personnel but also more broadly that in effect federal funding was being abused ... and that really he or his department needed to investigate these allegations," Mr Wilkie said.

"I never heard back from the minister on the allegations I raised with him so I can only assume no action was taken," he said, adding he was "disappointed" Mr Hunt did not launch an investigation.

In a statement to the ABC, a spokesman for Mr Hunt said: "Concerns were raised with the Tasmanian Government to ensure the program was meeting its stated objectives."

Fox situation morphed into 'much bigger issue'

"We are very fortunate to apparently be fox free," Mr Wilkie said.

"We do need to have a program which includes keeping a careful watch out for foxes getting into the state.

"[But] this situation about foxes in Tasmania now has morphed into a much bigger issue about governance and about the proper expenditure of public funds."

The fox eradication program was disbanded by the new State Government in 2014, but is still receiving federal funding earmarked for foxes as part of a broader invasive species program.

"The department is required to formally report to the Australian Government and spending is in line with the Project Agreement," Tasmania's Primary Industries Minister Jeremy Rockliff said in a statement to the ABC.

State independent MP Ivan Dean this year asked police to investigate alleged misconduct or fraud within the eradication program.

Police have said they were unable to lay criminal charges. The Tasmanian Integrity Commission is considering whether to launch an inquiry.

In late October a dead fox was found on the side of a highway in Tasmania's north.

Biosecurity Tasmania has ruled that the fox had been brought in from Victoria.

A Tasmanian man has been questioned as part of the investigation.