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Public servants protest over problems with the Phoenix pay system outside the Office of the Prime Minister and Privy Council in Ottawa on Oct. 12, 2017.Justin Tang/The Canadian Press

Unions representing more than 225,000 federal public servants appealed directly to the prime minister on Friday for an order to block the government from collecting more money from its employees than they received in overpayments through the troubled Phoenix pay system.

The leaders of 17 unions also demanded compensation be paid to civil servants for the suffering they've endured as a result of the pay crisis.

The demands, contained in a letter to Justin Trudeau signed by all 17 bargaining agents, coincide with this month's second anniversary of the launch of the electronic pay system and were issued ahead of protests planned for Feb. 28.

Since the launch of the Phoenix system in 2016, tens of thousands of federal employees have been underpaid, not paid at all or overpaid.

Those who received overpayments were told to report the mistakes before mid-January or risk having to repay the gross amount paid – in some cases amounting to tens of thousands of dollars – rather than the net amounts deposited to their bank accounts.

The unions say civil servants should not be required to repay more than they received.

"Therefore, we ask that your government grant a remission order to exempt federal public service employees in receipt of overpayments from repaying the gross amount and only require them to pay the net – the same amount they actually received," the letter to Trudeau states.

The Prime Minister's Office did not directly respond to the letter, but a spokeswoman for Public Services Minister Carla Qualtrough said the department hoped to close as many overpayment files as possible before government employees have to file their 2017 taxes.

"As we approach tax season, Public Services and Procurement Canada's priority is to process overpayments as quickly as possible," Christine Michaud said in a email.

Late Thursday, the department which oversees Phoenix issued a statement, telling government workers it's not too late report overpayments, but assuring them they would not have to pay back money that was not received.

Under federal tax laws, the department explained, some employees may be asked to repay the gross amount of their overpayment, depending on when the overpayment was processed.

However, since no repayments will be required until at least July 2018, employee tax accounts should be credited with the difference between the amount of overpayment they actually received and the amount they were asked to repay, said the PSPC statement.

"No employee will be out-of-pocket for any amount above what was deposited into their account by the employer."

Many civil servants have complained of stress and spending countless hours online or on phone calls trying to sort out their pay problems.

Those employees should be compensated for their time and the strain the issues have placed on their private lives, said the unions.

"Our members no longer have any confidence in the pay process thanks to Phoenix," the unions wrote in their appeal to Trudeau.

"We ask your government to accept that it owes its employees compensation for the suffering they have endured and continue to face."

The Phoenix system, initially approved by the previous Conservative government, was supposed to streamline pay for public servants across the country and save taxpayers an estimated $70-million annually.

But the government's latest estimates indicate the total cost of the system will likely rise to nearly $788-million by the end of March.

Auditor general Michael Ferguson says fixing the troubled Phoenix pay system should be a top priority for the federal government

The Canadian Press

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