After reaching a tentative contract deal with the federal government over the weekend, the head of the Professional Institute of the Public Service of Canada has doubts about whether members will receive money owed to them in a timely manner because of the government's ongoing Phoenix payroll problems.

The federal union, which represents scientists, auditors, information technology experts and other public service professionals, reached a tentative deal with the federal government to replace expired contracts for 18,000 of its members.

If accepted, thousands of members will receive a five per cent pay hike over four years, or 1.25 per cent each year. The deal is retroactive to 2014, when the previous contract expired.

But given the trouble-plagued Phoenix pay system, it is unclear how long processing those payments might take.

Since the federal government rolled out the Phoenix system in the spring, tens of thousands of federal workers have reported issues with their paycheques.

Many of those problems have had to do with supplementary pay, such as for extra duties, overtime or pay adjustments. Union president Debi Daviau is concerned the retroactive pay negotiated will also present problems.

Treasury Board asked for extension

Daviau said the contract states employees should get back pay within four months, but added she's "not that confident" the government will meet that deadline.

Daviau said the Treasury Board of Canada asked the union for a nine-month extension to process the retroactive payments, but the union rejected that request.

"We did not agree. [We] unanimously did not agree to that extend that period," she said.

"The necessity to keep the pressure on to fix the system and not simply avoid needing to use the system was appropriate."

Daviau stressed the retroactive payments will only be processed once all the other ongoing Phoenix pay issues for employees are settled.

Negotiations are still ongoing for about 32,000 members of the union.