Investigators also found apparent violations of aboriginal communities' policing agreements with the federal government.
The documents come to light following a recent decision by the governing Conservatives to renew the soon-to-expire program for another five years. The findings of the audits raise questions about the level of oversight in the $122-million-a-year program.
The federal government pays about half the cost of policing close to 400 First Nations and Inuit communities across Canada, while the provinces and territories pay for the rest. The program, which started in 1991, covers the cost of about 1,250 officers, who serve more than 338,000 people.
Public Safety Canada hired Toronto-based firm Ernst and Young to audit several of the government's policing agreements with First Nations and Inuit communities. The Canadian Press recently obtained those documents under the Access to Information Act.
Twelve audits were done between 2009 and 2012. While they covered just a fraction of the 163 policing agreements with First Nations and Inuit communities, the fact that Ernst and Young investigators consistently found the same kinds of problems in different parts of the country hints at a broader problem.
"It doesn't surprise me," said Scott Clark, a Ryerson University criminology professor who studies aboriginal justice issues. "It's a reasonably common problem — not just with First Nations organizations and not just policing.
"One of the problems in my experience is that whether it's self-government or whatever, First Nations take on responsibilities, and rightfully so, but very often, at the beginning anyway, don't have the capacity — particularly the administrative capacity — to really manage in the way that the federal funding agency would want them to manage."
Indeed, the auditors' biggest gripe was missing paperwork.
Personnel files in several of the communities lacked documentation to show officers had done their basic police training, were Canadian citizens, held valid drivers' licences or were trained to use firearms, pepper spray, batons and other weapons.
"Other than noting the social insurance number of the employee, no evidence of Canadian citizenship was on file," one audit said.
"Three employee files did not have evidence of the completion of basic police patrol program or special constable training program."
The First Nation later provided auditors with proof of the officers' training, as well as photocopies of Indian status cards for three officers and one passport. Other communities found some or all of the missing documents after the auditors pointed out they were missing.
Background checks were another problem.
Two of the audited First Nations communities failed to vet members of their police boards by doing criminal-record checks and verifying their education and credentials.
As well, all nine members of one police oversight board were elected officials, such as chiefs or councillors, which ran afoul of their policing agreement.
"The current structure is not in compliance with the agreement," the audit said.
Public Safety is drawing up a new agreement to allow elected officials to serve on the board, it added.
Investigators also found "a lack of review and sign-off" on work done by the financial controller, who signs cheques and handles payroll, and "inconsistencies" on time sheets.
The council stood by its decision to appoint elected officials to the police board, saying "the current board is comprised of elected chiefs of the member representative communities, all of whom possess the requisite knowledge, skill and ability to serve as a board member to govern our police service."
Public Safety declined an interview request.
It is rare a First Nation would purposely violate its policing agreement, Clark said.
"There is rarely, if ever, ill-intent to contradict agreements," he said. "I think it largely comes down to a question of capacity. The requirements placed on these communities by the funding agencies in terms of the paperwork is just phenomenal."