In the days leading up to Hunter Tootoo's resignation from cabinet a secret cabinet document under his watch was lost, CBC News has learned.

Details about the search for the missing file are laid out in a security incident report and obtained by CBC News through an Access to Information request.

Although some parts of the report are redacted, it shows staff frantically searched for the file when they realized the document was unaccounted for.

According to the report, several sensitive files were signed out on Tootoo's behalf ahead of a parliamentary affairs cabinet committee meeting on May 2.

Mr. Tootoo has returned every cabinet document he ever had. We have nothing further to add - Spokesperson for Nunavut MP Hunter Tootoo

"The documents were signed out to the minister and were signed for by [a staff member] who works in the minister's office and takes care of his cabinet committee meeting binders," the report said.

The report said several additional sensitive files were also prepared for Tootoo and were signed for and "were provided in an approved yellow cabinet documents folder. The minister's office was then responsible for ensuring the documents were provided to the minister in time for the meeting that afternoon."

Hunter Tootoo meets with Nunavut constituents this month after returning to work following a stay in rehab. (Sima Sahar Zerehi/CBC)

According to logs kept by the minister's office, all documents were returned on May 5.

But when staff later went to retrieve sensitive files for a routine audit, one file was missing.

"When I went to prepare for the audit on the former minister's account on May 26, I noted the document [redacted] was not amongst the documents in the safe," wrote the security officer who prepared the report.

The report said the staff member in the minister's office was asked to search the office and her files, but could not find anything.

"I also went through all of the drawers in the safe where the cabinet documents are secured and did not find it. I looked behind the drawers and went through the safe containing the DM's (deputy minister) account in case it had mistakenly been put in the wrong safe. I also went through all binders in Marian's (staff member) office in case it was not taken out and through all of the extra yellow cabinet document folders in Marian's safe," the officer wrote.

"I did not locate the document," the report concludes.

Tootoo says all documents returned

Tootoo was unavailable for an interview, but a statement from his office said "Mr. Tootoo has returned every cabinet document he ever had. We have nothing further to add."

Frank Stanek, a spokesman for Fisheries and Oceans, confirms the department realized a document was missing during "a routine audit of cabinet documents in May 2016."

But Stanek said the document went missing from the department and not the minister's office.

"The missing document was signed out of the minister's office by a department official, and subsequently could not be located. However, we can assure you that no sensitive information was compromised."

Stanek added the department has "taken appropriate measures to prevent this from reoccurring."

After CBC News published this report, Stanek sent a further email to say the missing document had nothing to do with Tootoo's departure from cabinet.

Tootoo resigned his cabinet post and left the Liberal caucus five days after the sensitive file was reported missing.

Tootoo said at the time he was resigning to deal with an addiction issue. Later, he clarified the real reason he left was because of an "inappropriate but consensual" relationship with a staff member.

Not first case of lost cabinet files

Cabinet documents are considered highly sensitive and great care is taken to ensure they remain confidential.

When files have gone missing in the past, significant political repercussions followed.

In 2008, then foreign affairs minister Maxime Bernier resigned after he left files at his girlfriend's apartment.

At the time, Prime Minister Stephen Harper said "it's a very serious error for any minister ... The minister immediately recognized the gravity of that error."

Bernier returned to cabinet following the 2011 election and is currently a candidate in the Conservative Party leadership race.

In 2009, an aide to then natural resources minister Lisa Raitt resigned after secret ministerial briefing documents were left in a newsroom.