At least two provincial Metis groups came under scrutiny after questions arose about their management and finances, newly released documents show.

Audits of the British Columbia and Saskatchewan organizations have come to light as their national council is embroiled in a controversy over its own expenses that has bred animosity among its top leadership.

Both Metis groups insist they have since dealt with the issues raised in their audits.

The Aboriginal Affairs Department hired an outside consultant to look at the Metis Nation Saskatchewan and the Metis Nation British Columbia. The Canadian Press obtained copies of the two audits, both done in 2012 by Ottawa-based Hallux Consulting, under the Access to Information Act.

Hallux is the same company that Aboriginal Affairs hired around the same time as the provincial groups' audits were done to take a closer look at the management practices and financial controls of the Metis National Council.

The Saskatchewan audit raised questions about executive compensation and travel, while the B.C. audit found apparent conflicts of interest and expenses that should have been ineligible for federal funding under the terms of their contribution agreements with the government.

Metis Nation Saskatchewan president Robert Doucette, who has been critical of the national council, said all the issues in the Hallux audit have been dealt with.

"If I'm going to be pointing fingers, I'd better be ready to answer other questions, too," Doucette said.

"It swings both ways and I'm OK with that."

However, Gerald Morin, a rival of Doucette who is a member of the elected provincial Metis council, said he does not know if the auditor's findings have been addressed.

Metis Nation British Columbia president Bruce Dumont was not immediately available to comment on the audit. In a recent interview, however, Dumont said his organization has dealt with the issues raised by the auditor.

"We had a chance to respond to our audit, of course, and we did straighten that out," he told The Canadian Press last month.

"There was a couple of things we had to deal with."

Another provincial Metis organization also fell under the microscope several years before the latest round of audits.

Unrelated documents, obtained from Health Canada under access-to-information, show the Metis Nation of Ontario Secretariat was audited in 2008 over "allegations of potential wrongdoings related to expenditures claimed by MNO under the funding agreements."

That audit, done by Navigant Consulting, found the Ontario group claimed $260,827 that "was either not supported by documents or considered ineligible expenses under the terms and conditions of the funding agreements."

A memo to Health Canada officials says the findings for its department are of financial mismanagement rather than wrongdoing.

Two other departments -- Heritage Canada and Human Resources and Social Development Canada -- were involved in the audit. Part of a paragraph that presumably describes how the findings relate to those departments has been censored in the copy provided to The Canadian Press.

Gary Lipinski of the Metis Nation of Ontario, who became president after the audit was done, said the organization repaid the expenses flagged by Navigant when he took over.

The organization has made plans to repay its other creditors and since 2008 has paid back a significant amount of its debt, he added.

"There are problems and they need to be fixed and we need to change, and so MNO has done that. I would say that I believe that we are one of the most transparent aboriginal governments in Canada right now."

Last week, the B.C. Metis Federation -- a rival group to the Metis Nation British Columbia -- wrote to Aboriginal Affairs Minister Bernard Valcourt to express concern about the results of an investigation into the national council.

They were responding to a Canadian Press report that revealed for the first time details of investigations that raised red flags over the Metis National Council's management practices and financial controls. Areas of concern included questionable contracts and apparent conflicts of interest.

The federation said the probes raise what it calls "a number of very serious issues that demand immediate answers and full public disclosure."

National council president Clement Chartier and vice-president David Chartrand of the Manitoba Metis Federation say some of the findings in a Hallux draft report were flawed and other issues have since been resolved.

However, the rest of the council's board of governors are at odds with Chartier and Chartrand, saying they didn't know about the issues flagged by Aboriginal Affairs and do not want to be associated with the probe's findings.