Canada's auditor general says the $520 million in outstanding Phoenix pay claims revealed in his fall audit on Tuesday does not give the entire scope of the problem, because his team was not given pay information for all the departments using Phoenix.

Michael Ferguson said he did not have access to unresolved pay information from 55 federal departments and agencies who process pay using the Phoenix pay system but not through the Miramichi pay centre.

"There would also be outstanding transactions for the other 55 departments, but those numbers aren't collected by Public Services [and Procurement Canada]," said Ferguson after his fall audit report was presented to parliament on Tuesday.

Michael Ferguson

Auditor General Michael Ferguson held a news conference at the National Press Theatre in Ottawa Tuesday to discuss findings in his 2017 fall report. (Sean Kilpatrick/Canadian Press)

Ferguson said those additional departments, including the Canada Revenue Agency and Canadian Border Services Agency, represent 30 per cent of the government's workforce.

The auditor general said the Treasury Board Secretariat is currently collecting that information from the missing departments, but a request from CBC News to that department late Tuesday did not produce any further data.

'I think the picture is actually worse'

The unions representing public servants spoke out about the report Tuesday afternoon.

"I think the picture is actually worse," said Robyn Benson, president of the Public Service Alliance of Canada, the largest union representing federal workers.

"We were never able to get the actual figures which is really disconcerting."

The president of the Professional Institute of the Public Service of Canada, Debi Daviau said she was disappointed in the auditor general's report and the missing data.

Debi Daviau PIPSC Phoenix newser Ottawa Jan 12 2016

Debi Daviau, president of the Professional Institute of the Public Service, says the government should scrap the Phoenix pay system. (CBC News)

"The auditor general is really talking quite large numbers and they're not even the whole picture," said Daviau. "And yet he's coming to a very strange conclusion in that we should continue to invest all this time and money into a system that my members tell me is simply not fixable."

Last week, Daviau's union, which represents 15,000 IT specialists, urged the government to scrap Phoenix and go with plan B — a newly built, in-house, pay system.

"I don't think we need more study at this point, I think we've studied this thing to death and that's what's led us to the conclusion that it's simply time to pull the plug," said Daviau.

First priority is stabilizing

Carla Qualtrough, the minister in charge of Public Services and Procurement Canada and the Phoenix file, doesn't discount the professional institute's advice, but she said the first priority is stabilizing the pay situation.

"We're also exploring longer term options that may or may not result in Phoenix being the long-term solution. But to be very clear, we cannot defer any resources away from stabilizing, we have 300,000 people we need to pay every two weeks," said Qualtrough.

She acknowledged that payment issues are still on the rise, and said this is because the federal government recently negotiated 20 collective agreements that had been left to expire. The collective agreements added a significant number of new transactions to the Phoenix pay system, she said.

Carla Qualtrough

Carla Qualtrough, minister of Public Services and Procurement Canada says her department is exploring "longer term options" for the pay system that may or may not result in keeping Phoenix. (CBC)

"Over the past month we've paid $614 million to public servants in retroactive payments related to collective agreements," Qualtrough said in an interview with CBC Radio's Ottawa Morning.

The number of problems would be going down if it wasn't for this bump in transactions, she added.

"Ninety per cent of public servants are covered by these collective agreements, there's a multiplicity of transactions because it's four years of retroactivity in some cases."

Qualtrough also took the opportunity to once again blame the previous Conservative government for deciding to build the new pay system in the first place.

The minister said the government accepts Ferguson's report and all of its recommendations and has already taken steps to fully implement them.