Rosanna Di Paola is the associate assistant deputy minister responsible for the federal government's Phoenix pay system. (supplied) IBM is being paid for its work on the multi-million dollar contract for the new public service payment system, even as hundreds of federal public servants have been left without paycheques or underpaid for weeks or months at a time, according to a senior federal manager.

"The system is working. So they got paid for work done," Rosanna Di Paola, the associate assistant deputy minister responsible for the federal government's problem-plagued Phoenix pay system told CBC Radio's Ontario Today on Thursday.

"The issues we're having are more procedural than they are technical. Phoenix will only pay out what it knows about, so the system itself is functioning as designed. We've tested the system inside and out."

Meanwhile a temporary federal payment centre is up and running in Gatineau, Que., to deal with a big backlog of requests from government employees who aren't being paid properly.

The issues we're having are more procedural than they are technical. - Rosanna Di Paola, senior federal manager

The federal government's main public service payment centre, in Miramichi, N.B., couldn't handle the volume, Di Paola said.

"We've set up the satellite centre with very experienced compensation advisors who can help us muddle through the backlog and get people paid," Di Paola said.

"We do want people to be paid and we're doing the utmost we can to put mechanisms in place for people to get paid."

The bulk of the backlog relates to employees who aren't receiving their pay increments, she said.

However CBC News has heard from dozens of federal employees experiencing a variety of pay problems ranging from underpayment to overpayment to no payment at all, sometimes for months. Employees in special circumstances such as those returning from maternity leave and sick leave are reporting long delays in getting their pay back on track. And many employees complain the system set up to help them through the mess is unresponsive and ineffective.

"These stories are frightful and they're not what we're about in the federal public service," said Di Paola.