About 10,000 cases of current and former public servants having problems getting paid properly remain in the federal government's backlog, and the overall cost for fixing the Phoenix pay system this year could rise above $50 million.

"Our progress remains slow because of the complexity of the various cases, but we're nearing a significant mark," deputy minister Marie Lemay told reporters at a technical briefing held in Ottawa Wednesday morning.

The "vast majority" of cases involving employee terminations and leave without pay have been dealt with, Lemay said,  adding that those categories are important because they involve overpayments and could have tax implications. A total of about 14,000 overpayment cases were identified by the government in mid-October.

The remaining backlog is mainly made up of employee transfers, she added.

Federal employees began reporting problems with their pay soon after the Phoenix payroll system was rolled out across the country in the spring. The government has acknowledged that about 82,000 public servants reported trouble, with the majority being underpaid.

On Nov. 29 — about a month after the government's self-imposed deadline to resolve the 82,000 cases of people being underpaid, overpaid or not paid at all — Public Services and Procurement Minister Judy Foote told a House of Commons committee that about 15,000 unsolved cases remained.

Still not meeting standards

In a given month the Phoenix system gets about 83,000 new pay requests from the 46 departments it serves for things like promotions, creating accounts for new hires and final payments for departing workers. Lemay said Wednesday that the government is not meeting the 20-day standard for processing them.

Instead, it's taking more than three months.

But processing times are improving as pay centre workers become more familiar with the system and as the backlog is cleared, Lemay said.

Satellite pay centre offices will remain in operation as long as necessary, she added.

In September, the government said the Phoenix problems would cost taxpayers about $50 million this year.

Lemay said Wednesday that it could rise above that mark because satellite units might be kept operational longer, among other things.

A review of the Phoenix system could take until the spring of 2017 to complete, Lemay said. A decision about whether to give bonuses to the executives behind Phoenix will be made once the results of the review are in.