Joe Friday was appointed on March 27, after serving at the office as deputy commissioner since 2011 and general counsel since 2008.
That experience isn't seen as a positive to people like former public servant and whistleblower Alan Cutler, with the group Canadians for Accountability.
"Joe Friday, even if he wants to move forward he's at a disadvantage," said Cutler. "He's got to shake that old baggage off and he's going to have to prove it's gone."
The Conservative government established the commissioner's office in 2007 as a means of providing protection for whistleblowers in the wake of a 2004 auditor general report and subsequent investigations into the sponsorship scandal, which revealed widespread abuse in how Public Works officials awarded government contracts.
But it has had a troubled history.
1st commissioner resigned after scathing audit
Christiane Ouimet, the first federal integrity commissioner appointed by Prime Minister Stephen Harper, resigned in 2010 before a scathing audit found she had failed to fulfil her mandate and had mistreated her staff.
Her successor, Mario Dion, vowed to clean up the office, but he tabled just 10 reports to Parliament in four years.
Friday told Robyn Bresnahan on Ottawa Morning he doesn't think the office has been mismanaged but said there have been "growing pains" and challenges that he has tried to learn from.
"I believe fundamentally in the role and the mandate of this office, and... I wanted to spend the rest of my public sector career working in this extremely important, innovative and in many ways groundbreaking field," said Friday.
Advocates like Cutler, who was a whistleblower during the sponsorship scandal, says his group's experience with the office is one of "continual frustration."
David Hutton, another whistleblowing advocate, has also criticized the office for avoiding big cases in favour of "small potatoes" complaints.
"There's almost never any finding of a systemic problem other than a case of a few bad apples," said Hutton.
'We weren't created as a police force'
But Friday disputes those characterizations, and says issues with the office arise in part because of a misunderstanding of their mandate.
"We've got teeth," said Friday.
"We weren't created as a police force... we are not an ombudsman office, we don't represent an individual, they can have their own legal counsel.
"We represent the public interest... we advocate on behalf of whistleblowing, not necessarily on behalf of an individual whistleblower," said Friday.
Friday says his to-do list includes pushing for changes to the Public Service Disclosure Act. A review of the act is three years overdue.- Listen to Robyn Bresnahan's interview with Joe Friday Suggest a correction