A senior federal civil servant overseeing the problem-plagued Phoenix payroll system has told public servants who are not getting paid properly to ask their departments for emergency cheques.

"Really there is no reason for employees not to get paid," Brigitte Fortin, assistant deputy minister with Public Services and Procurement Canada, said in a technical briefing with reporters. "Where employees' pay is delayed, departments and agencies can issue salary advances."

While some of the problems lie with her department, Fortin pointed out that some employees and managers are unfamiliar with the new system, or may have delayed inputting data into the new program.

Yet the Public Service Alliance of Canada said this week that hundreds of public servants still aren't getting paycheques and the government's toll-free help line has been swamped with calls. The union is also urging employees to request priority pay if they have not received their wages on time.

Fortin told reporters the government has just hired 50 people to answer the phones and brought in 40 new compensation advisers.

As for the problems with Phoenix, Fortin said the department subjected the new payroll system to rigorous testing for 18 months and submitted it to 16,000 different pay scenarios.

A worker with the Department of Oceans and Fisheries tosses a sockeye salmon back into the water northeast of Vancouver. Colin Barnard, who works for the department in northern B.C., had to dip into his RRSP because he hadn't been paid since February. (Andy Clark/Reuters)

"We encountered some issues with particular types of pay such as shift work," she said. "These problems have been fixed. As well, we've seen some very specific problems with certain departments such as the coast guard where employees have unique work schedules.

"So we have fixed issues for the coast guard employees and we are continuing our work," she added during the briefing.

People surviving on loans, RRSPs

Yet James Stensrud told CBC News today that he still hasn't received a cent of top-up pay since he went on paternity leave in mid-February. The Canadian Coast Guard worker said he has been forced to ask his family for loans.

Amber McCoy, an employee at Health Canada, hasn't received a regular paycheque since the introduction of Phoenix. She said she's getting by on a line of credit and emergency cheques from petty cash at work.

Colin Barnard works at a Department of Fisheries and Oceans spawning channel in northern B.C. and had to dip into his RRSP this month because he hadn't been paid since February. He said he recently received two small emergency cheques.

The Canadian Coast Guard icebreaker Sir ‎William Alexander seen in Port au Choix Harbour. Coast Guard worker James Stensrud told CBC News he's had to ask his family for loans since he hasn't received his top-up pay since February. (Submitted by Kim Ploughman)

And Keyvan Abedi at Citizenship and Immigration told CBC he's been shortchanged $900 every month since the introduction of Phoenix two months ago. When he complained, Abedi received an email that told him "the service standard for this case is approximately 40 business days."

"Why do you roll something out that's so complex to so many departments in such a short time. Like two months? For an IT system across so many departments? It makes no sense," Abedi said.

Problems arose after system was live

Fortin called the introduction of Phoenix a major undertaking that is necessary to replace a pay system that had been in place since the 1970s.

She said work on the transition began in 2009, and when the system wasn't ready to go as planned last spring, Public Services and Procurement Canada decided to delay implementation.

"We knew we would encounter some challenges. These challenges could only be identified once the system was in use and exposed to a broad range of pay scenarios," Fortin said.