The Privy Council Office released a letter to the RCMP on Sunday saying it had been mistaken when it originally told investigators that Perrin's emails were deleted, in keeping with standard procedure, when he left the job in March.
In fact, Perrin's emails were already being preserved in connection with an unrelated matter, says the letter, which is signed by Isabelle Mondou, assistant secretary to the cabinet in the office of the counsel to the Clerk of the Privy Council.
"Upon Mr. Perrin's departure at the end of his employment in late March 2013, the PMO was provided a notice that his emails had been deleted from the computer server," Mondou writes.
"On Nov. 29, 2013, we found that Mr. Perrin's emails had in fact been retained due to a litigation hold in an unrelated matter."
Perrin's name appears repeatedly in RCMP documents released two weeks ago containing explosive allegations about a scheme to repay Sen. Mike Duffy's disallowed housing expenses and whitewash a Senate report into the controversy.
The documents allege senior PMO staffers — including Nigel Wright, Prime Minister Stephen Harper's former chief of staff and the man who paid Duffy's $90,000 bill — were involved in trying to work out a deal with Duffy to repay his expenses and worked with top Tory senators to change a report on Duffy after unsuccessfully trying to shape an independent audit into his expenses.
In May, Perrin denied that he was ever consulted about, or participated in, Wright's decision to cover Duffy's expenses, and said he never communicated with Harper about it.
But emails disclosed by the RCMP in documents filed in court show Perrin was intimately involved in negotiations with Duffy's lawyer, Janice Payne, who set out five conditions — including full reimbursement — that had to be met in return for Duffy's admission that he mistakenly claimed a housing allowance to which he was not entitled.
Indeed, Wright at one point emailed Duffy in exasperation, saying that if the senator continued to misquote him, they would converse in future strictly through their lawyers, Perrin and Payne.
The deal originally involved the Conservative party reimbursing Duffy for repaying his expenses, while curtailing an audit into his claims. Conservative Fund chairman Irving Gerstein, also a senator, initially agreed to reimburse Duffy when the tab was thought to be only $32,000 but balked when it became clear it was upwards of $90,000.
At Wright's behest, Gerstein also solicited information from a contact at auditing firm Deloitte about the status of their report on Duffy.
The RCMP alleges that Wright and Duffy committed bribery, fraud and breach of trust in cooking up the deal. The allegations have not been proven in court, and no one has yet been charged.
However, last week, University of Ottawa law professor Amir Attaran filed a complaint against both Perrin and Payne with the law societies in British Columbia, where Perrin now teaches law at UBC, and Ontario, where Payne practices. He claims the duo "violated the ethics of the profession" in helping to craft an illegal deal between Wright and Duffy.
Perrin has engaged legal counsel and has declined all comment.
Duffy has also refused to comment on the latest allegations. Wright maintains he acted within the scope of his position as chief of staff and remains confident his actions were legal.
The new cache of Perrin emails could shed further light on his involvement in the transaction.
The Privy Council Office says it will "immediately turn over these email records" to the RCMP and that it has apologized to both the RCMP and the Prime Minister's Office.
"We regret that we previously failed, even if inadvertently, to accurately inform you and the PMO about the availability of Mr. Perrin's emails," Mondou writes. "We apologize for any inconvenience it may have caused."
Harper has steadfastly maintained that he was kept in the dark about the scheme until learning May 15 that Wright had repaid Duffy's expenses, and has been laying the blame squarely at their feet. But a compelling series of emails between various PMO operatives, including Perrin, suggest details of the plan were more widely known than Harper has suggested.
Wright resigned from the PMO in May, shortly after the details of the payment emerged. But other senior staff in the PMO, including director of issues management Chris Woodcock and manager of parliamentary affairs Patrick Rogers, were also active in the discussions about how to get Duffy to repay his expenses, the documents show.
Both are still with the government: Woodcock works for Natural Resources Minister Joe Oliver, Rogers for Heritage Minister Shelly Glover.