OTTAWA—Repairing the federal government’s public service pay system is a top priority, the newly minted minister responsible for the Phoenix payroll service insisted Monday, just hours after her department revealed that a backlog of problem pay files has grown over the last several weeks.

“The prime minister has given me, made this a priority for me, in our discussions already and I look forward to being briefed and working to remedy this as soon as possible for public servants who have been waiting so long to get this fixed,” Carla Qualtrough said shortly after being named by Justin Trudeau as public services and procurement minister.

Qualtrough’s appointment came just hours after the department revealed the pay system’s problems worsened since the backlog of improper pay cases was last tabulated July 26, as employees struggled to process changes to civil service contracts.

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The number of pay transactions carried out through the Phoenix pay system that went beyond normal processing times increased by 9,000 from that date to 237,000 after two months of decline, according to the newly released figures.

As part of a small cabinet shuffle Monday, Trudeau announced Qualtrough would replace Judy Foote, who resigned from the public services portfolio last week for family health reasons.

Foote had been on temporary leave from the cabinet post since April and the role of overseeing Phoenix had been handled temporarily by Natural Resources Minister Jim Carr.

Qualtrough’s new department had been whittling the backlog down since June, when it had reached 265,000 pay transactions that went beyond the normal monthly workload of approximately 80,000.

The number of problem files dropped to 228,000 by late July before rising again over the last four weeks.

Officials blamed the increase on the need to shift pay system employees to handling pay changes resulting from the ratification of several big public service contracts, many of which went into effect in late June.

“This increase was expected as we focused our efforts on ensuring employees are paid what they are owed as a result of recent collective agreements and within legislated timelines,” said a statement from the department.

The 19 collective agreements signed so far — with another eight to come — require the government to make retroactive payments, enact salary increases and pay other allowances negotiated as part of the new contracts, all within legislated timelines.

“To meet these timelines, we dedicated a number of compensation advisers to work almost exclusively on these payments,” the department said.

“This shifting of resources affected our ability to reduce the number of pay transactions at the Public Service Pay Centre.”

The department said it expected the situation to continue into the fall, suggesting the backlog could get worse before it gets better.

The former Conservative government introduced the new pay system as a way to standardize how federal employees are paid across the country.

Phoenix was also expected to save millions of dollars as the electronic system was supposed to streamline transactions.

However, the system has been plagued with problems, leaving tens of thousands of federal employees underpaid, overpaid or in some cases not paid at all — sometimes for months.

The government earlier in the summer estimated that fixing the problems and eliminating the backlog could cost $400 million over at least two years.

The department also revealed Monday that it had increased the percentage of pay transactions carried out within the government’s service standard of between 20 and 45 days, to 49 per cent as of Aug. 23, compared with 35 per cent a month earlier.

And it noted that pay transactions for employees on maternity or parental leave, as well as disability transactions, were being processed within 20 days, 95 per cent of the time.

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Still, the government acknowledged Monday that more needed to be done to resolve the problems.

“The pay issues currently being experienced by public servants are unacceptable and we are working collaboratively at all levels to resolve them,” said an emailed statement from a department official.

“Ensuring all employees are paid the money that they have earned remains our priority. We are making all necessary efforts to reach a steady state as quickly as possible.”