The federal government all but confirmed it will not meet its self-imposed Oct. 31 deadline to deal with a backlog of Phoenix payroll issues despite doubling down on the promise just two weeks ago.

Marie Lemay, the deputy minister in charge of the file, said the government is "tracking a bit behind," with 30,000 out of more than 80,000 cases still unresolved with less than two weeks to the deadline.

Lemay said the "bulk" will be cleared in time but that some of the most complex cases — those requiring "time-consuming, manual calculations" — might not.

"We're still driving for the 31st. We're going to give it our best shot," she said during a Wednesday afternoon update on the payroll mess. "We continue to make progress but we still have much work to do."

Federal public servants began reporting problems when the system launched, and by July 2016, the government acknowledged that more than 80,000 workers had reported trouble with their pay, with the majority being underpaid. Others were overpaid or not paid at all.

Some cases "date back several years" and require more research, said Lemay.

"It is important to note that we're focused on speed, as well as care. We must make sure that we're not creating new problems by solving old ones."

The government's deadline is for dealing with the cases filed by federal workers before July — not new cases filed later.

The government has also committed to dealing with new, high priority cases within two weeks of the claim, and new priority cases within six weeks of the claim.

849 new priority cases

Lemay said during the last update on Oct. 5 that the government had resolved 38,228 cases and was "on target" to meet the Oct. 31 deadline. On Wednesday, she said an additional 12,824 cases had been resolved, for a total of more than 51,000 cases closed.

Since the last update on Oct. 5, Lemay said there have been 894 new priority cases. Those cases were prompted by employees going on maternity or parental leave, or employees leaving the public service.

"The majority of these employees are still receiving their salary but have yet to be transitioned to employment insurance or pension," she said, adding that these priority cases would be addressed within six weeks.

There have also been 79 new cases that are not considered high priority — all of which have been resolved or will be resolved by the next pay period, she said.

Wednesday's technical briefing is the first since Rosanna Di Paola, the bureaucrat who oversaw the Phoenix pay system for years, was shuffled into another role at Public Services and Procurement Canada.

Lemay said Di Paolo has "worked diligently to launch Phoenix over the last three years," and remains a member of her executive team.