Next tax season could be especially frustrating for the more than 80,000 government workers affected by the Phoenix pay system, warns an Ottawa accountant.

Government workers in various departments have complained about not being paid, being underpaid, or in some cases being overpaid.

"For people living paycheque to paycheque there's no words for what they're going through," said Charles Ghadban, a chartered professional accountant and certified management accountant.

Charles Ghadban, a chartered professional accountant, says the issues with the Phoenix pay system with stretch into tax season.

"More than just the basic problem of putting food on the table and making mortgage payments and paying your bills… When it comes to taxes I could see people being taxed at a much higher rate even though they may not have made that much money."

He said people's T4s will be "thrown out of whack" and that could mean they'll be taxed at 35 to 40 per cent, compared to 20 per cent.

An incorrect T4 will also have a ripple effect on deductions including employee's CPP contributions, employment insurance contributions and group benefit, explained Ghadban.

People are going to be up in arms and revolting. - Charles Ghadban

"It can be substantial. It's going to be a nightmare for the Canada Revenue Agency," he said. "People are going to be up in arms and revolting."

Ghadban also foresees situations where people will be forced to withdraw chunks from their savings, including RRSPs, to survive. In that case the money will be taxed.

Track everything

"How is the government going to reimburse them? Are they going to reinstate their RRSP room? Are they going to give them their money back? It's going to be an administrative nightmare for the government," he said.

Ghadban said a few years ago the government issued a special kind of form, a T1198, for federal employees who were paid retroactively.

Charles Ghadban says tax season will be a "nightmare" for CRA next April. 1:31

"So they may have to institute pretty much the same kind of solution," he said.

Here's some advice to make next April less brow furrowing:

Separate bank accounts: If you're part of the group being overpaid, Ghadban suggests putting that money in a separate account and prepare to return it. Note your fines: If you're being paid or it's inconsistent, keep track of the money you've spent drawing from your RRSP fund, loans and/or interest fees. "I'm sure those people are going to be reimbursed somehow," said Ghadban. Track how much you're getting paid: Ghadban recommends keeping a tally of how much you should be receiving each pay period against what you're actually receiving. That way you can tell the Canada Revenue Agency what the discrepancies are.

Phoenix was introduced in early 2016 for some departments. About 720 public servants — mostly new hires and students — have contacted the government about not receiving pay. Another 1,100 have not received parental, long-term disability or severance payments, while more than 80,000 employees entitled to supplementary pay for extra duties, over-time or pay adjustments have had problems.