Prime Minister Justin Trudeau says he has tasked the country's top civil servant with overseeing a troubled system that has botched paycheques for 80,000 federal workers.

"It's something that I have engaged in personally and tasked the clerk of the privy council to oversee. We are making sure that this situation gets fixed," Trudeau said, referring to Michael Wernick, whom he named to the role last January.

"We are making sure that this situation gets fixed," Trudeau said Wednesday morning in Gatineau, Que.

Federal officials revealed at a briefing earlier this week that more than a quarter of the federal public service is affected by the new Phoenix system, which is supposed to handle pay cheques for all 300,000 workers. More 720 workers haven't been paid in months, while another 1,100 on parental or sick leave are receiving the wrong pay. The vast majority are being overpaid or aren't receiving overtime and "acting" pay for filling in for another worker.

Have you had problems with the Phoenix pay system? Email us.

Asked whether someone will be held accountable for the problems, Trudeau said his government is now focused on fixing the situation.

"There will be time to talk about lessons learned down the road. But we are taking this very, very seriously and ensuring that people get the support and the pay that they are owed," he said.

Marie Lemay, the deputy minister of Public Services and Procurement, said earlier this week that the government will evaluate the rollout and its ensuing problems, and committed to making the evaluation public. The government has also asked Auditor General Michael Ferguson to examine Phoenix.

Civil servants from across the country have emailed Â鶹´«Ã½ about the problems they've encountered with Phoenix. Many have said they'd prefer not to be interviewed, fearing retribution for speaking out or simply citing rules that discourage public servants from speaking to journalists without permission. They say they've racked up credit card bills or had to take loans to pay their mortgages, and spend hours on the phone trying to reach the pay centre. Some have also said they're getting conflicting information about when they'll be paid or to what stage their case has progressed.

One woman told Â鶹´«Ã½ she has had irregular paycheques since March when her Indigenous and Northern Affairs Canada internship ended and she started a new contract. Since then, she's had varying amounts on her paycheques. One June paycheque was for several thousand dollars, but ensuing paycheques were for much smaller amounts - $449 or even zero dollars.

"I just want to be able to understand it," she said. "I don't know if they're adding up. It's so silly."

"If in June I was paid $6,000 for the missed pay that I was owed, I thought it was all cleared up, but now they're taking away that overpayment. It's ridiculous."

The woman says her partner has been able to cover their mortgage, so she's luckier than a lot of public servants who are experiencing similar problems.

But, "After five months of this going on, I'm just extremely frustrated," she said.

A news report Tuesday revealed the Phoenix system also breached workers' privacy by allowing 70,000 managers to see the private information of all public servants.

Annie Trepanier, a spokeswoman for Public Services and Procurement Minister Judy Foote, told Â鶹´«Ã½ that the incident was viewed as low-risk. Foote wasn't made aware of the privacy breach until last week, despite four departments discovering it last January.

Trepanier said in an email that the government put in place "a system fix" following the January incident to prevent it from happening again.

"Following established protocol, the department reported the incident to the Office of the Privacy Commissioner of Canada and Treasury Board Secretariat‎," Trepanier told Â鶹´«Ã½.