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The Public Service Pay Centre in Miramichi, N.B. Nearly one-third of the public service have experience payroll issues since the federal government launched its new Phoenix pay system.The Canadian Press

As the federal government whittles away a backlog of payroll problems caused by its new pay system, officials say new payroll entries are taking an "unacceptable" amount of time to process.

The deputy minister in charge of dealing with the Phoenix pay system debacle says about 18,000 backlogged cases have yet to be processed, down from roughly 22,000 files that were still on the books two weeks prior.

But Marie Lemay says a secondary backlog of sorts was created over the summer months as payroll processing times slowed to about 40,000 files per pay period.

The deputy minister of Public Services and Procurement Canada says the goal is to ensure that federal workers are paid what they are owed within 20 days of submitting their regular pay claims.

But while pay processing times have vastly improved, Lemay says that target is being achieved only about 20 per cent of the time as a result of the earlier slowdown.

The remaining 80 per cent of employees are being forced to wait for payments for up to two months or even longer.