The largest union representing federal public service workers is filing a complaint against the government for missing a collective agreement deadline, likely because of ongoing issues with the Phoenix pay system.

The Public Service Alliance of Canada says it will file the complaint with the Federal Public Sector Labour Relations and Employment Board Wednesday. The Treasury Board has already admitted it will not meet the latest deadline to pay three years worth of back pay under four collective agreements as well as increase wages.

The new agreements were signed June 14, 2017 with a 150-day implementation deadline.

'Adds insult to injury'

Greg McGillis, PSAC regional executive vice-president for the National Capital region says many public servants were depending on the back pay set out in the collective agreement. (CBC News)

McGillis believes the deadline wasn't met because of ongoing problems with the Phoenix pay system.

"From the beginning, [the government has] been very close-mouthed about exactly what the cause is. I think we can just assume it's Phoenix," he told CBC News.

From the beginning, [the government has] been very close-mouthed about exactly what the cause is. I think we can just assume it's Phoenix.' - Greg McGillis, PSAC regional executive vice-president

The failure to implement the wage adjustments even comes after the government had two extra months to implement the agreements, which usually have a 90-day deadline, McGillis said.

PSAC is looking for compensation for both the persistent problems with Phoenix and the failure to implement these new agreements.

Just how much they ask for in damages will depend on how long it takes before the issue is resolved, McGillis said.

Some people are living paycheque to paycheque and have been racking up interest payments or late payments and were depending on this back pay, he said.

The government had said in October that pay centres across the country were making the collective agreement changes a priority — ahead of other Phoenix issues.

"Of course there are problems with Phoenix, and of course it's unconscionable what's happened and it's terrible and our members still aren't getting paid. This adds insult to injury," said McGillis.

No timeline for Phoenix fixes

In Question Period Tuesday, NDP public services and procurement critic Erin Weir asked whether the government would rebuild a publicly administered payroll system to fix the Phoenix "boondoggle."

Public Services and Procurement Minister Carla Qualtrough responded that the problems are her department's top priority.

This is a frustrating and unacceptable situation that we're being totally transparent on and we're working hard to fix. - Scott Brison, Treasury Board President

"While we did not create this problem, we are fixing it," she said.

On Tuesday, Treasury Board President Scott Brison also acknowledged the frustrations public servants face, but wouldn't give a timeline as to when collective agreements would be implemented.

"It's just totally unacceptable that we are not able to pay our public servants on time, or accurately in many cases," he said.

Treasury Board President Scott Brison wouldn't give a timeline of when the collective agreements would be implemented. (CBC News)

"This is a frustrating and unacceptable situation that we're being totally transparent on and we're working hard to fix," said Brison, adding the complexity of the agreements that need to be implemented has burdened the pay system.