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The Public Service Pay Centre in Miramichi, N.B.The Canadian Press

The federal government has missed its self-imposed deadline for clearing a backlog of payroll problems and is now looking to get things sorted out by the end of the year.

Marie Lemay, deputy minister of Public Services and Procurement Canada, says there are still about 22,000 cases to be dealt with.

That's down from 82,000 recorded during the summer.

The advent of the government's new Phoenix payroll system left thousands of public servants with problems.

Some were underpaid, some were paid too much and others weren't paid at all.

Lemay says she is disappointed that the backlog couldn't be cleared sooner.

"We desperately wanted to reach our target," Lemay told a briefing Monday. "I want you to know we will continue to work tirelessly to close the remaining cases as quickly as we can."

She said she's looking at year-end as the new target for clearing the backlog.

"We're organizing all of our work, from all the transactions, the backlog also, to minimize tax implications, because the end of the year is really important and we're going to putting a lot of focus on that."

Lemay said the cases that remain are complicated and require time-consuming hand calculations. Some problems pre-date the implementation of the Phoenix system.

The government budgeted $50 million to clear up the payroll problems and Lemay said that hasn't changed.

Another $1 million was earmarked to set up and run an office to help departments reimburse employees for out-of-pocket expenses caused by pay problems, but the final cost of the claims office is expected to be about half that, said Alfred Tsang of the Treasury Board.