Prime Minister Justin Trudeau knew about former cabinet minister and Liberal MP Hunter Tootoo's intimate relationship with an office staffer, but kept quiet to protect her identity, a spokesman says.

The Prime Minister's Office told reporters on May 31 that Tootoo had voluntarily resigned his ministerial duties — and would be leaving the Liberal caucus — to seek treatment for addiction issues. Trudeau, too, avoided specifics at the time and said, "This was [Tootoo's] own choice after a very difficult situation," when pressed by reporters.

But no mention was made of what Tootoo himself has called an "inappropriate but consensual" relationship with an underling in his employ.

The PMO conceded Thursday it knew the circumstances all along, but only commented after Tootoo told CBC News further details about his abrupt resignation.

"Hunter Tootoo acknowledged to the prime minister that he had been engaging in what was an inappropriate relationship in the workplace," a spokesperson said in a statement. "Mr. Tootoo informed the prime minister that he took full and sole responsibility for his inappropriate workplace conduct."

A PMO spokesperson affirmed Thursday that the prime minister and his top advisers opted to keep those details from the media, and in turn the public, because they did not want the name of the woman to be disclosed.

Tootoo's revelation about the relationship also helps explain why he was treated markedly different than a former caucus colleague, Newfoundland MP Seamus O'Regan, who also entered rehab to seek treatment for alcoholism earlier this year.

O'Regan never left the Liberal fold during his stint in rehab, and he received positive words of encouragement from Trudeau. "My thoughts are with my friend and colleague @SeamusORegan tonight, and he has my full support," the PM tweeted shortly after O'Regan's disclosure.

Not forced to keep quiet by PMO

Tootoo said he "voluntarily" told Trudeau on May 31 about his situation, and that he was never pressured to keep his relationship secret by anyone in the PMO.

"No I wasn't," he said. "My interest is in protecting the individual involved. I'm not going to get into any details. I'm ashamed of what I've done and I'm deeply sorry."

It's not clear if the relationship with the staffer is ongoing, but Tootoo said she asked him to refrain from mentioning her name.

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Hunter Tootoo apologizes for 'inappropriate relationship'1:31

The former cabinet minister faced a barrage of questions about the relationship after the Globe and Mail initially reported Tootoo's sexual involvement with a staff member, but he repeatedly evaded those questions.

"I know that there's lots of rumours and allegations out there," he said after the report initially surfaced. "The fact of the matter is that I recognize that my issue was with alcohol, and there's been some deeply personal and private issues that have haunted me, and unfortunately alcohol is a coping mechanism for dealing with trauma and I've been personally affected by those impacts."

Tootoo will not resign

Jack Anawak, a former Liberal MP who ran for the NDP in Nunavut in the last election, said Tootoo should have set boundaries with his co-workers and has handled the situation "poorly."

"It's inappropriate. I don't think that we should be condoning that at all," he said of the relationship with a staffer.

He called on Tootoo to step down as an MP and run again in a byelection. "I don't think we're going to be properly served by an independent member of Parliament. He's not going to have the influence."

Anawak also said he doesn't believe Tootoo stepped back from cabinet, and the Liberal caucus, on his own volition without any influence from the PMO.

"I think there are very few times people step down voluntarily ... from a fairly high level cabinet position," Anawak said.

Tootoo has said he will not resign despite the inappropriate relationship and the Liberal Party's insistence that he will not be allowed to return to caucus. "I'm not about to turn around from a difficult path ahead; I always face challenges head on," he said.