OTTAWA -- Prime Minister Justin Trudeau says Canada’s major institutions aren’t doing enough to prevent toxic and unsafe workplaces, including the Canadian Armed Forces, which today ushered in the first-ever female second-in-command.

Speaking to reporters on Tuesday, Trudeau said recent reports from various federal entities are "really troubling," and in light of that, he welcomes the new appointment of Lt.-Gen. Frances J. Allen as Canada’s next vice chief of defence staff.

"I’m very pleased to see a strong woman in the vice chair position for the first time in Canada’s history and obviously the task of everyone in senior leadership in our military is to move forward on ending the challenges of harassment and discrimination in the military and other systems as well as ensuring that anyone who comes forward to share stories or allegations is given the support and resources they need," he said.

His statements come against the backdrop of ongoing investigations into the behaviour of two top military leaders – former chief of the defence staff Gen. Jonathan Vance and his successor Admiral Art McDonald.

Military police launched an investigation into sexual misconduct allegations against Vance in early February, 2021, following his retirement. CTV News has not independently verified these allegations. Shortly after, Defence Minister Harjit Sajjan announced that McDonald was "voluntarily" stepping aside while an investigation into unspecified allegations of misconduct against him is ongoing.

"I think what we’re seeing over the past days, weeks, and months is a really troubling pattern in Canada, whether we talk about the news coming out of the Canadian Armed Forces, whether we talk about the [Michel] Bastarache report into the RCMP, or even recent reports coming out Correctional Service Canada," he said.

"This needs to end."

Conservative Leader Erin O’Toole is calling for an entirely independent investigation into the Vance and McDonald allegations and a freeze on all promotions and salary increases for the general and flag ranks.

"It’s a historic institution for our country. There is eroding trust right now and we have to save it. It’s not going to be from some press release from the current minister, we have to show swift and serious action for the men and women wearing uniform," he said during a press conference on Tuesday.

"So far I’ve seen the Liberals more worried about avoiding responsibility than showing that the Canadian Armed Forces needs to be an institution that is preserved and respected."

O’Toole also welcomed Allen to her new role, adding that he “served alongside some incredible women during my time in the Canadian Armed Forces.”

Allen had been seen as a possible contender to take over from Vance as Canada's first female defence chief, before McDonald was selected for the job.

She most recently served as Canada's military representative to NATO headquarters in Brussels and is the second woman to have attained the rank of lieutenant-general in the Armed Forces.

She's taking over as vice-chief from Lt.-Gen. Mike Rouleau, who had been in the running for the acting chief of defence staff position, a job ultimately given to Lt.-Gen. Wayne Eyre.

The senior leadership shuffle was announced by Eyre Tuesday morning.

"Each leader will go on to represent Canada, whether at home or abroad, in key decision making positions," he said in a statement. "The responsibilities of shaping the CAF of the future are great."

NDP Leader Jagmeet Singh also weighed in on Allen's historic appointment stating that while it has an "incredible positive impact" for representation in the military, one single appointment won't alone create systemic change.

"It can't just be brushed aside and it goes right to the top, it goes to the prime minister as well. It's his responsibility to make sure women are safe in the military and that is the opposite of what's happened so far, " said Singh on Tuesday.

The House of Commons national defence committee is also conducting a study into sexual misconduct in the Armed Forces.

With files from The Canadian Press.