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Jarrad Yardon, a student working for the Department of National Defence, was finally compensated after waiting seven months for pay.Dave Chan/The Globe and Mail

Hundreds of federal public servants who missed entire paycheques due to problems with the new Phoenix compensation system received their back pay on Wednesday, according to the government.

As promised, Ottawa fully compensated some of the most severely affected cases – 486 of the 720 public servants who hadn't receive paycheques. However, there still appear to be glitches with the pay system.

Jarrad Yardon, a student who works at the Department of National Defence in Ottawa, said he assumes he is one of the 720 public servants the government prioritized for compensation. He didn't receive any paycheques from January to May, and has had inconsistent pay since then.

After some last-minute meetings with human resources staff this week, the $3,900 owed to Mr. Yardon by the government finally landed in his bank account on Wednesday. However, the fight with his employer is not quite over. An error in his file led the Phoenix system to overpay him by $500 for vacation he did not earn; the money will be clawed back from his next paycheque in two weeks.

"As soon as the pay goes through for the next pay cycle and hopefully the $500 is recovered without any further issues, then I'll safely say that I'm out of the woods for the rest of this contract," said Mr. Yardon, whose term ends in August.

He said he can now make his tuition payments for his final year at Carleton University and pay off past-due bills. However, he hopes the government will eventually compensate him for the interest accrued on bills and the damage done to his credit rating as a result of the pay problems, or he may have to consider legal action.

"Another thing that was suggested to me … was to pursue the matter through small claims [court]," Mr. Yardon said. "It's something that I could look into if they [the government] don't actually follow through with further remedies like they say they're looking into."

Public Services and Procurement Minister Judy Foote visited the government's central pay centre in Miramichi, N.B., on Wednesday, and said the roughly 200 employees who missed paycheques this time will have to wait until the next payday in two weeks because of incorrect or incomplete information entered by their departments. The Phoenix system oversees the payment of 300,000 federal public servants.

The employees paid Wednesday are only a handful of the more than 80,000 who have missed paycheques, or been overpaid or underpaid since Phoenix launched in February. The government has said it will be months until all of the cases are resolved. Reporters will likely hear more about the government's timeline at a technical briefing with department officials in Ottawa on Thursday.

The House of Commons government operations committee will also hold an emergency meeting Thursday to examine the Phoenix problems, following demands from the Conservatives and NDP to do so. The committee will decide how to proceed with the study, including from whom it will hear testimony. Ms. Foote is not scheduled to appear before the committee at this time.

The pay fiasco has recently escalated to new levels. Smoke inside a federal data centre shut down the Phoenix system, government e-mail and some websites on Wednesday. The system was back up and running in the afternoon, although the government's central IT department did not say how long it was offline.

Last week, the federal Privacy Commissioner announced a formal investigation into a privacy breach linked to Phoenix earlier this year. Shortly after the system launched, several managers in different departments reported being able to see personal information of employees from other departments. The Privacy Commissioner's office said it is unclear how many employees were affected.

Ms. Foote has also asked Auditor-General Michael Ferguson to review the planning and implementation of Phoenix. In the meantime, 13 public service unions are taking the government to Federal Court over the matter to seek a ruling that it must pay public servants properly and punctually.

With a report from The Canadian Press

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