Another costly problem is emerging in the wake of Ottawa's troubled rollout of its new computerized payroll system.

The two largest unions representing federal public servants are owed hundreds of thousands of dollars each in union dues that have not been properly collected since Phoenix was rolled out.

"Our priority continues to be getting our members paid," said Debi Daviau, president of the Professional Institute of the Public Service of Canada.

But she describes the union's funding hit as "significant" and is worried the union will have trouble representing its members properly if the issue isn't fixed.

"We're already quite tight for money... we're not a business that has a whole bunch of money in reserve that we can access, and therefore we need a timely remittance of dues," Daviau said.

PIPSC, which represents 55,000 federal workers, says it is owed about $300,000.

Debi Daviau, the president of the Professional Institute of the Public Service of Canada, says her union can't afford not to receive accurate union dues collected by the federal government's troubled new payroll system. (CBC News)

The Public Service Alliance of Canada, which represents 170,000 employees, is owed more than PIPSC, but a representative did not have an estimate available.

"We certainly know that our union dues have not been correct since February," said Chris Aylward, the national executive vice president of PSAC.

But Aylward says his organization's operations are still running at full capacity.

"It's certainly not impacting our priority at this point. Our priority at this point is our members getting paid."

Public Services and Procurement Canada confirmed there is a problem with union dues.

"Public Service and Procurement Canada is aware of the dues remittance issues with certain bargaining agents," said Me'shel Gulliver Bélanger, a spokesperson for the department.

"PSPC and TBS (Treasury Board Secretariat) are currently collaborating with our federal bargaining agents and we are committed to resolving this issue‎ as soon as possible."

Ottawa has been trying to resolve pay issues for more than 80,000 federal workers since implementing a new payroll software system, called Phoenix, earlier this year.

Formal complaints launched

PIPSC has taken several steps to have this issue addressed.

Policy grievances have been filed against several government departments that employ unionized workers, including the Treasury Board, the Canada Revenue Agency and the Canadian Food Inspection Agency.

An unfair labour practice complaint is also expected to be filed in the coming weeks at the public service labour relations board.

"We're not at the point where our members are at, which is passing the hat around the office in order to survive, and therefore our members continue to be our priority at this point," Daviau said.

Trifecta of problems halts dues collection

There are three separate factors affecting the unions' ability to collect dues.

The first, and most obvious issue, is that when members are not paid, dues cannot be withheld.

Chris Aylward, the national vice president of the Public Sector Alliance of Canada, says his union hasn't been receiving accurate union remittances since February. (Submitted)

"Members could find themselves, many months in, in arrears in dues and that's totally unfair," Daviau said.

The second problem relates to new hires, who are not being properly processed by the Phoenix system.

PIPSC says it is not being notified about hundreds of new employees and therefore it is unable to collect dues from those new members.

The third, and most complicated factor, is a change to when and how dues are collected.

For years, Ottawa delivered union dues on a monthly basis.

But the system has been changed to make those payments every two weeks.

This means the union gets half of what it would normally receive when an employee leaves a job half-way through a month.

The issue will likely be addressed when members of both unions meet with Public Works Minister Judy Foote on Aug. 19.