A newly released federal report estimates the problem-plagued Phoenix payroll system has already cost Canadian government coffers more than $1 billion and could require an additional $500 million a year until it is fixed.

The majority of future spending is being described as "unplanned" costs and doesn't include more than $120 million in expected, one-time expenses.

The report says the government's best estimate is that it could take five years to stabilize the Phoenix pay system.

It is also a snapshot in time as of March 2018.

Public Services Minister Carla Qualtrough, who oversees work on the system, says she expects the actual costs to be lower over time given some improvements and pilot projects the government is implementing.

Since it launched, Phoenix has resulted in countless public servants being overpaid, underpaid or not paid at all and a backlog of cases for officials still to resolve.

The comptroller general's report says it is unlikely for any system to have a backlog queue of zero, noting that there will always be ongoing errors or issues to resolve.

Auditor general Michael Ferguson lambasted the system last month in a report that called Phoenix an "incomprehensible failure" of project management and oversight, which led to green-lighting a system that wasn't ready.

Privy Council clerk Michael Wernick fired back at Ferguson during a Commons committee hearing this month, accusing the auditor of making "sweeping generalizations" about public servants.