At least 80,000 public servants have had trouble getting the compensation they are owed because of major problems in the government's new pay system, Phoenix, and it will be months before all of the issues are resolved.

Department officials said that of the 300,000 public servants paid through the Phoenix system, 81,820 – nearly a third – have been affected since it went into operation in February. Speaking to reporters in Ottawa on Monday, Public Services and Procurement Canada deputy minister Marie Lemay said departmental staff in Gatineau, Que., and Miramichi, N.B., where the main pay centre is based, are working around the clock to get the problems fixed.

Under the new system, the affected public servants have missed paycheques, been over- or underpaid, or denied health benefits. It is not clear why these workers were affected.

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"I am deeply concerned about the pay problems being reported by public servants," said Ms. Lemay, who joined the department April 11. "Ensuring that our staff are paid what they earned is our top priority. This situation is completely unacceptable."

While Ms. Lemay repeatedly expressed disappointment over the pay issues, she refused to say whether those responsible would be disciplined or fired. She said the department will evaluate the process. Public Services and Procurement Minister Judy Foote has asked Auditor-General Michael Ferguson to review the planning and implementation of Phoenix.

The Canadian Taxpayers Federation said accountability is needed for the Phoenix problems.

"Certainly some form of sanction is probably appropriate. At a private company, this sort of incompetence would have consequences, and it should in the public sector as well," said Aaron Wudrick, federal director of CTF.

Of the 300,000 public servants paid by Phoenix, 80,000 have not received supplementary pay such as overtime or pay increments. Another 1,100 public servants leaving the government for reasons such as maternity leave, disability leave or retirement also reported problems, while 720 have missed entire pay cheques.

Ms. Lemay said the department's priority is paying those 720. On July 27, 486 of them will be fully compensated, and the remaining cases will be dealt with as quickly as possible.

Next up will be the 1,100 people who have left the public service and not received compensation such as severance pay. Ms. Lemay said these cases will be dealt with in a "matter of weeks."

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Finally, the 80,000 public servants who are waiting on supplementary pay will be dealt with in the coming months. Ms. Lemay said that timeline is dependent on the number of new workers the government can hire at its temporary pay centre, which was set up in Gatineau last month.

The government had planned to hire 100 for Gatineau, but only 56 are currently working there, according to Ms. Lemay. That number will grow to 89 in the coming weeks. The government has struck a deal with the Public Service Alliance of Canada (PSAC) to hire workers for the Gatineau centre who had been laid off by the Conservative government in cutbacks. Ms. Lemay said they are hoping to have a total of 150.

Ms. Lemay also announced on Monday that the phone line capacity in Miramichi will be increased, and "technical enhancements" will be made to Phoenix to allow departments to view their transactions in the system so they can help resolve pay issues stemming from incomplete or inaccurate information.

However, Phoenix is not the crux of the problem. Ms. Lemay said the government underestimated the time and training needed to move to the new system.

She said the government is also considering compensating public servants for expenses incurred due to improper payment, including late fees – a demand public service unions have made.

Thirteen public service unions are taking the government to Federal Court over the matter, seeking a ruling that the government must pay public servants properly and punctually. After Monday's technical briefing, PSAC vice-president Chris Aylward said his union is considering taking further action against the government as the Phoenix problems continue, but did not expand on the union's specific plans.