Top Conservatives, including former prime minister Stephen Harper, kept silent about sexual-misconduct allegations involving Rick Dykstra even as the former Tory MP rose in the ranks of Ontario politics – a decision that is now revealing deep fractures in the federal party.

Recent revelations that members of Mr. Harper's inner circle debated whether to remove Mr. Dykstra as a Conservative candidate in the 2015 election over sexual-assault allegations have exposed a massive rift in federal Tory circles that has spilled into the provincial level after Patrick Brown stepped down as leader of the Ontario Progressive Conservative Party over allegations of sexual misconduct.

On Feb. 2, Maclean's magazine reported on a series of private, high-level e-mails between Mr. Harper's most powerful aides. The e-mails raise questions as to why no one spoke publicly about Mr. Dykstra's alleged behaviour until now – more than two years after it was first brought to their attention.

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Three sources have told The Globe and Mail that a conference call between top aides and Mr. Harper was held to discuss Mr. Dykstra's candidacy in the 2015 election, and it was the former prime minister himself who decided Mr. Dykstra should stay on.

In a statement released late on Friday, Mr. Harper called for a full investigation of the allegations, but did not say Mr. Dykstra should have been dropped as a candidate. Mr. Dykstra lost his seat in St. Catharines, Ont.

"When allegations were brought to my attention during [the] 2015 election campaign, I understood that the matter had been investigated by the police and closed a year prior," Mr. Harper said in the statement.

"Given this understanding of the situation, I did not believe that I could justify removing him as a candidate. Recently, much more information has come to light, including information to the effect that the original investigation may not have been complete. In my view, it is essential that criminal allegations, including this one, be fully investigated and prosecuted if warranted."

But just who knew what and why the details of the allegations were kept under wraps for more than two years has emerged as a major point of contention among those who were once Mr. Harper's closest and most powerful aides.

It also calls into question why those who were aware of allegations did not raise concerns when Mr. Dykstra ran for president of the Ontario Progressive Conservative Party in early 2016. He held the high-profile position until his resignation last week a few hours before Maclean's posted its January story alleging he sexually assaulted a young female staffer in 2014.

Mr. Dykstra has denied the story through his lawyers. The alleged victim declined to speak to The Globe and Mail. Before his resignation, Mr. Dykstra was part of the party executive that decided to hold the PC leadership race in March, before the Ontario election this spring.

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Mr. Brown was forced to resign after CTV aired a report that two women accused him of sexual misconduct during his time as a federal MP, allegations he has denied.

One of the women, then a 19-year-old junior member of Mr. Brown's staff, told CTV she had been drinking and went into the MP's bedroom with him, where he kissed her and laid down on top of her. After she told him she had a boyfriend, she said, Mr. Brown stopped and drove her home.

The second allegation dates from a decade ago when a woman said she met Mr. Brown at a bar when she was under Ontario's legal drinking age and was drunk. Mr. Brown, a teetotaller, invited the woman and her friend to his home. The woman told CTV the MP made unwanted advances after he offered her a tour of his place. Neither of the women reported the allegations to police.

The report about the e-mails detailing the discussions of senior Conservatives have led some political insiders to speculate the story first leaked to bring Mr. Dykstra down in the aftermath of the Brown affair. The Globe and Mail has not viewed the e-mails first-hand but has verified their authenticity.

According to a report in January, a staffer who worked for a different Conservative MP filed a police report in 2014 alleging Mr. Dykstra had sexually assaulted her by forcing her to perform oral sex on him after a party. She took her concerns to the party whip's chief of staff, and the matter eventually came to the attention of Conservative Party lawyer Arthur Hamilton and the Tory war room.

Loyalty among Mr. Harper's aides is now split between former campaign manager Jenni Byrne and campaign chair Guy Giorno, who are at odds over who failed to address the allegations.

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Ms. Byrne's allies say she advocated most strongly for removing Mr. Dykstra, and that Mr. Giorno and senior campaign operative Ray Novak were only interested in legally insulating themselves; Mr. Giorno's camp says he, too, suggested dumping Mr. Dykstra at one point and that Ms. Byrne did not inform the prime minister about the allegations for a week during the campaign.

Mr. Giorno denies knowing the allegations involved assault until the account was published in Maclean's late last month, despite the fact that Ms. Byrne referred to a sexual assault to describe the alleged action in an e-mail she sent to the senior campaign staff.

After telling The Globe last week that the campaign never discussed the future of Mr. Dykstra's candidacy, Mr. Giorno now says he didn't remember because he no longer had the e-mails from the time of the campaign. He maintains that he was unaware of the specifics of the sexual misconduct allegations against Mr. Dykstra.

"I should have asked what it meant. I don't recall asking what it meant, I don't recall an answer," he said. "I don't recall any decision-making discussions or being present for them. If I was there, I hope I would have taken a position consistent with my position in the e-mails which was dumping him.

"I think he should have been dumped," he said.

In a statement posted to Twitter on Friday, Mr. Novak said he knew police had investigated a complaint about Mr. Dykstra and that it had been closed without charges. Mr. Hamilton attempted to investigate the matter, but there were no charges and the complainant asked for privacy, he said.

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"The matter was not taken lightly by anyone involved, and any suggestion to the contrary is misleading and false. This was an extremely difficult decision that ultimately turned on whether a closed investigation without charges was sufficient grounds for firing," he wrote. "Certainly, with the benefit of hindsight and additional information, Rick Dykstra should have been fired as a candidate. But campaigns don't get do-overs."

Both Mr. Novak and Ms. Byrne said they welcome the third-party investigation launched by federal Conservative leader Andrew Scheer last week.

"I look forward to participating in the process," Ms. Byrne said in a statement.