OTTAWA — Canada’s top military officer temporarily stepped aside as chief of the defense staff after military police opened an investigation into unspecified allegations against him.

The removal of Adm. Art McDonald came in the midst of a separate investigation into the previous chief of the defense staff, Jonathan Vance, a now retired army general. Reports surfaced this month that he behaved inappropriately with two female subordinates.

“I take all allegations of misconduct seriously and continue to take strong action on any allegation of misconduct that is brought forward,” Harjit Sajjan, the defense minister, said in a statement released late Wednesday night on Twitter. “No matter the rank, no matter the position.”

The Ottawa Citizen, citing unnamed sources, reported that a victim and several witnesses have charged that Admiral McDonald engaged in sexual misconduct.

Canada’s military has long struggled with allegations of sexual misconduct and sexism.

In 2019, the government set aside $690 million to settle claims of sexual harassment and misconduct within its military brought in five class action lawsuits. The settlement followed an external review by a retired Supreme Court justice who found that military had “an environment that is hostile to women and L.G.T.B.Q. members, and is conducive to more serious incidents of sexual harassment and assault.”

Earlier this week, the Conference of Defense Associations Institute, a Canadian policy group led largely by former military officers, issued a statement raising concerns about the effect sexual misconduct allegations are having on the military.

“Allegations of this nature erode public trust in the Canadian Armed Forces, and ultimately negatively affect morale and harm efforts to recruit the future protectors of our nation,” the group said.

During his tenure, Mr. Vance, who served as defense chief from 2015 to until his retirement last month, launched a highly publicized program to “ensure sexual misconduct is never minimized, ignored or excused.”

When Admiral McDonald was sworn as chief of the defense staff, he spoke about the need to change the culture within the military and apologized to its members “who have experienced racism, discriminatory behavior and or hateful conduct.” He told reporters that over his career he had unintentionally perpetuated some of the problems that he now planned to address.

But less than a month into his new job, Admiral McDonald faced criticism after posting a tweet promoting diversity and cultural change containing a photograph of eight white senior military commanders around a table with a single woman in civilian clothes and a ninth man appearing on a video screen behind them.

Lt. Gen. Wayne D. Eyre, the commander of the army, will temporarily act as the military’s top officer.

Citing the police investigation, Mr. Sajjan, a former lieutenant colonel in the army who served in Bosnia and Afghanistan, declined to offer any specifics. The Department of National Defense also did not offer any details.

Last week, Mr. Sajjan declined to tell the House of Commons committee on national defense when he first learned about the allegations against Mr. Vance, only saying he was “shocked” when they were first aired publicly by Global News, a Canadian broadcaster, earlier this month.

Mr. Vance, who twice led the Canadian Forces based in Kandahar, Afghanistan, was appointed by the previous Conservative government.

On Sunday, Global News broadcast an interview with Kellie Brennan, a former army major, who said that she had a sexual relationship with Mr. Vance over several years, including periods when she was under his command in Toronto and Ottawa.

When asked if it was consensual, Ms. Brennan said: “On a personal level, ‘consensual’ meaning was I participating in it? Yes.”

But she added: “Could I say no to him? No. The reason why I say that is because if he rang me on the phone or if he texted me, I was obliged to get back to him.”

She said that her attempts to raise the issue within the military went nowhere.

“It was a hot potato that nobody knew what to do with,” she said.

Mr. Vance denied having sex with Ms. Brennan while she was under his command, but said that they had dated in 2001.