The federal government apologized Monday for a mammoth problem with its new pay system that has impacted more than one-quarter of its roughly 300,000 employees, some who say they've been forced into dire financial circumstances.

Some 400 civil servants can expect emergency payments by the middle of next week but government officials said it could take months to fully correct the system.

In the meantime, the government is exploring ways it can compensate employees for out-of-pocket expenses resulting from the pay predicament, such as reimbursements for bank and credit card fees.

"I'll apologize to anyone who's suffering hardship, financial or other, with no problem," Marie Lemay, deputy minister of Public Services and Procurement, said.

"There's many elements and components of this system, and obviously the system is not working."

For months, civil servants have complained about being short-changed on their pay stubs, not being paid enough, or in rare cases being paid more than they should.

Some said they hadn't been paid in months, forcing them to max out credit cards, miss mortgage payments and default on student loans.

The problems first arose as a trickle of technical glitches when the government brought the new Phoenix pay program online several months ago, but quickly grew out of control.

"We accumulated a large backlog of unprocessed payment requests due to the learning curve for Phoenix users," Lemay explained.

"This is really the central reason why we are where we are. It is clear that we underestimated the amount of time that it would take for all users to become trained and familiar with the system."

The majority of problems involve about 80,000 civil servants who didn't receive proper compensation for overtime and other extraneous payments.

But officials said at least 1,100 employees have raised issues surrounding payments for maternity and other leaves and 720 employees have complained of receiving no paycheque at all.

Officials said 486 workers should receive emergency payments by next week, but it could take months for the government to fix all the problems.

Lemay also called Monday for employees experienced with payroll systems who've left the department to come back temporarily to help resolve the problems and deal with the backlog of cases.

Treasury Board President Scott Brison told a Commons committee in April the decision to consolidate pay operations in a new pay centre in Miramichi, N.B., was made by the previous Conservative government to replace a 40-year-old system.

But the government saw problems with the system in the early days of being rolled out and didn't listen to warnings that the second phase of introducing Phoenix to all departments was happening too quickly, said the Public Service Alliance of Canada.

The union, which represents the majority of federal civil servants, has already gone to court over the issue and is vowing to take "significant action" as early as next week if more urgent problems aren't fixed immediately.

Last month, Procurement Minister Judy Foote said she asked the auditor general to investigate what went wrong, suggesting the system may not have been tested enough before being launched.

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