Former prime minister Stephen Harper says that, on the basis of what he knew at the time, he could not justify dumping Rick Dykstra as a Conservative Party candidate in 2015.

Dykstra, a former Conservative MP, resigned as president of the Ontario Progressive Conservative Party last Sunday, hours before Maclean's magazine reported he had been accused of sexual assault in 2014.

According to the magazine, federal party officials allowed Dykstra to stand as a candidate in 2015 despite the allegation. Dykstra's lawyers have told Maclean's that the allegation is "false."

Earlier on Friday night, Ray Novak, Harper's former chief of staff, released a statement in which he said, with the benefit of hindsight and additional information, he wished the Conservatives had dropped Dykstra, but at the time there was not enough information available to make that decision.

Both men had not previously commented and their statements came just as Maclean's published a new story on the Dykstra case, quoting email exchanges between senior Conservatives during the 2015 campaign.

The story recounts testy exchanges among senior campaign officials about whether to drop Dykstra, with one, Jenni Byrne, arguing for his dismissal.

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In his statement, Harper said that when allegations were brought to his attention during the 2015 campaign, he "understood that the matter had been investigated by the police and closed a year prior."

"Given this understanding of the situation, I did not believe that I could justify removing him as a candidate," Harper said.

"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."

Novak now says the matter was "not taken lightly, and any suggestion to the contrary is misleading and false."

"During the 2015 campaign we learned that police had investigated a complaint against MP Rick Dykstra the previous year, and that the investigation was closed without any charges having been laid," Novak said in a statement late Friday.

"The campaign asked the Party's lawyer to investigate further but unfortunately the facts available at the time were few: a closed investigation with no charges and a complainant asking for privacy.

"This was an extremely difficult decision that ultimately turned on whether a closed investigation without charges was sufficient grounds for firing. 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."

Harper talks to his then chief of staff Ray Novak during a campaign stop at the shipyards in north Vancouver. Novak was the senior director of Harper's campaign tour. (Sean Kilpatrick/Canadian Press)

Novak served as chief of staff for two years, but was an aide to Harper for many years before that. He is now managing director of Harper & Associates, the former prime minister's consulting firm.

Conservative Leader Andrew Scheer has ordered an independent investigation into how Dykstra was allowed to remain a candidate in 2015. Novak said he welcomes that investigation.

"I fully support the review of how this matter was handled at the time, as well as the wider discussion currently taking place, in the hope it will assist future teams inside and outside politics in dealing with these situations in the best way possible," Novak said.

In the House of Commons on Monday, Conservative MP Michelle Rempel was scathing in her response to the allegations in the original Maclean's story.

"Is it possible for a drunk staffer to give consent for sex to a senior male in a workplace organization who aggressively propositions that staffer?" she asked.

"Media reports say that [Conservatives] sat around a very senior table and argued semantics around whether action in our workplace should be taken because criminal charges were not proceeded with.

"Those people should be ashamed of themselves," Rempel said.