The federal government paid nearly a quarter of a million dollars to a consulting firm for work on an independent analysis of the Phoenix pay system that was not given to the minister overseeing the project, CBC News has learned.

"The contract for Gartner Canada, completed in February 2016, was for $221,073.88," said Kelly James, a spokeswoman for the Treasury Board Secretariat.

Gartner Canada is one of two consulting firms hired by Ottawa to write independent reports on Phoenix, before the first wave of the pay system was rolled out in February.

Judy Foote, the minister of Public Services and Procurement, saw one of the reports but was never briefed on the Gartner report.

"It's absolutely a waste of taxpayers' money," said Chris Aylward, the national vice-president of the Public Service Alliance of Canada.

"When they go out and do these independent assessments, and they cost almost a quarter of a million dollars for one of them, and that's the one that the minister doesn't even see... a responsible minister would have said, 'do I have all of the information here?' Obviously Minister Foote didn't do that here," Aylward added.

Foote defended the staffers who did not turn over the second analysis.

"Both reports, by the way, said similar things, had similar concerns, but neither report indicated that we should not proceed," Foote said.

"What I'm told is that the concerns that were raised were actually addressed," Foote added.

CBC News obtained both reports, and the Gartner analysis offers a wider range of criticism than the document presented to the minister.

"I think this latest mishap is just emblematic of the Phoenix boondoggle," said Erin Weir, the NDP's critic of Public Service and Procurement.

"Taxpayers should be very concerned about this waste of money. I think the study was a good one, and might have been worth the money if the government paid attention to it," Weir added.

The 60-page document flagged concerns about "accuracy and timeliness of pay" and suggested slowing down the roll-out of Phoenix to mitigate risk.

For the Canadian Taxpayers Federation, this development raises another concern.

Aaron Wudrick of the Canadian Taxpayer Federation says the government should think twice when commissioning reports. (CBC)

"It suggested that it is either something that the minister should see at the very least so that we know that something came of that money, or it suggests when these types of reports are commissioned we need to think twice about exactly whether or not we need to do it," said Aaron Wudrick, the federal director of the CTF.

"I think somebody has some explaining to do for sure. At the end of the day somebody made a decision that was not a good one and in the private sector that would have consequences and it should here as well here too," Wudrick said.

Union to go after feds for unpaid dues

The unions representing public servants have not been able to collect their full dues because of problems with the Phoenix roll out.

PSAC estimates it is being short changed by $150,000 a month, and if the issue is not resolved by the end of the year the union could be owed as much as $1.5-million.

"We will be pursuing the government to recover those funds," Aylward said.

He explained the union is preparing to go after the Treasury Board and PSPC to get the money the union is owed.

"We won't be going back to the members to say you're already in a financial hardship because you haven't been paid, we're not going to back and say 'now you owe us $600,'" Aylward added.

The Professional Institute of the Public Service of Canada says it is owed approximately half a million dollars. PIPSC has not said if it will be going after the government to recover funds.

Both unions say the government has committed to finding a solution to the dues problem.

Since Phoenix was fully implemented in April, more than 80,000 public servants have come forward with pay problems.

Most have been underpaid, while some have been overpaid or not paid at all.

The department of Public Services and Procurement Canada has promised to clear the backlog by the end of October. But the backlog only includes workers who have come forward with problems before July 1, and there is no timeline for public servants who have dealt with pay troubles after that date.

There is also no timeline for when the system will work as intended.