Thousands of Canadian public servants have missed paycheques, been over- or underpaid, or have been denied health benefits since the roll-out of the government's new pay system, Phoenix, which went live in February.

Thirteen public service unions are now taking the government to Federal Court over the matter, seeking a ruling that will force the government to pay public servants properly and punctually.

Jarrad Yardon, who is on a student contract at the Department of National Defence (DND) in Ottawa, wasn't paid from January to May. Since then, his pay has been inconsistent, forcing him to rack up debt to pay overdue bills.

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Last week, things reached a breaking point when Mr. Yardon's boss dug into his own personal finances to help him out.

"One of my directors was generous enough to loan me money for groceries last Friday," Mr. Yardon said.

The Liberals, who inherited the system from the previous, Conservative government, have called in Auditor General Michael Ferguson to examine the planning and implementation of Phoenix.

"My top priority is to make sure that every employee who performs a job gets paid for the work that they have done. This is totally unacceptable," Public Services and Procurement Minister Judy Foote told The Globe and Mail on Friday.

Mr. Yardon, a 23-year-old Carleton University student, estimates the government owes him about $9,000 for missed paycheques. In May, he was provided with a stack of cash – $5,450 in $20 bills – as back pay for his four-plus months of employment.

Mr. Yardon estimates that he has made some 2,500 calls to the pay centre in Miramichi, N.B., since his problems began, only getting through a handful of times. As the tuition deadline for his final year of university creeps up, he's afraid he won't be able to pay his fees and go back to school, which is critical to maintaining his government job. He needs proof of enrolment to stay in the student worker program.

Constantly worried about being unable to pay bills, he has trouble sleeping at night. He started seeing a psychiatrist last week, who prescribed him sleeping pills.

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Going public with the matter was a tough decision for Mr. Yardon, who feared reprisals at work. The opposite has happened. He says his bosses have been supportive and Treasury Board President Scott Brison even called him to apologize for the matter. However, he still hasn't seen the rest of the money he's owed.

"If 'I'm sorry' could pay the bills, I would have retired and bought a beach house a long time ago."

Debi Daviau, president of the Professional Institute of the Public Service of Canada, said some public servants have lost their homes because they couldn't make mortgage payments. That's why the union recently began offering interest-free loans to members who can prove they have suffered financial hardship as a result of Phoenix's glitches.

On top of the money owed, Ms. Daviau said, those affected should be compensated for the damage done to their credit.

"How are they [the government] going to alleviate the bad credit situation that they've created for their employees?"

Ms. Foote said she doesn't know if this type of compensation will be possible, as each case will have to be considered individually. For now, she's focused on the immediate issue.

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The government has opened a temporary pay centre in Gatineau, Que., that employs 100 compensation experts. Ms. Foote said the centre will stay open until the backlog problems are resolved and the government will hire as many compensation experts as needed to get the job done.

Despite the government's efforts, Public Service Alliance of Canada (PSAC) vice-president Chris Aylward said the government's handling of the matter has been "a complete boondoggle." He said PSAC even warned the government against rolling out Phoenix before it was ready, but it went ahead anyways.

"They [the Liberals] can't simply say, 'Oh, this is a Conservative problem.' No, it's not," Mr. Aylward said. "They have got to do something concretely."

Mr. Aylward said the government should revert back to its old regional pay system while it takes Phoenix offline. Ms. Foote said Phoenix isn't going anywhere, as the system works. Rather, she said those using the system need better training. IBM, which designed Phoenix, would not comment.

Earlier this month, NDP public services and procurement critic Erin Weir wrote Prime Minister Justin Trudeau, urging him to "take immediate action" to fix the problems and provide a clear timeline for doing so.

"I think that Canadians would expect any workplace to pay its employees correctly and on time, so it's embarrassing that our national government isn't doing that," Mr. Weir said.

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Government officials will hold a technical briefing for journalists on the Phoenix pay system Monday in Ottawa. Ms. Foote said more details will be made available then, including a timeline for a resolution.