While the government has agreed to pay for the first check for staff hired before November last year, it will not fund subsequent checks or vetting for new employees.

Public service unions say the $71 fee is a sticking point in wage negotiations as the mandatory background checks affect tens of thousands of workers.

The government said on Monday it had heavily subsidised the tax-deductible fee, which workers will have to pay every three years.

Thousands of Canberrans who work with children have already undergone criminal background checks before a November deadline for the first phase of the new system.

The checks are compulsory not just for paid employees of organisations but for all people who volunteer in child care and child education services, justice facilities for children, child protection, child accommodation, counselling and support services for children and commercial services for children.

In the years to follow, all Canberrans who work with vulnerable people, not just children, will need to be registered.

The Community and Public Sector Union said it did not believe ACT government employees should have to pay for their own checks every three years.

While unions have broadly welcomed an improved wage offer from the government, the CPSU's ACT branch secretary, Vince McDevitt, said the registration charge could put the brakes on negotiations.

"This is potentially a barbecue stopper," he said. "The problem is that it costs money and they don't want to pay for it.

"We've got schools assistants, people at Bimberi [Youth Justice Centre] … this is potentially going to hit bus drivers. This will affect one-10th of Canberra's population."

Mr McDevitt said the government's one-off agreement to pay the registration fee for its staff in the first year of the new system was not enough. "They have created the legislation, the obligation and the onus," he said.

"I'm not arguing against the merit of it. But why should we pay it?"

A spokesman for Children and Young People Minister Joy Burch said the government was already absorbing a "significant cumulative cost" by paying for checks for workers hired before November 8 last year.

The spokesman said there was also no registration cost for volunteers. "For future employees who may have to pay the $71 fee it is worth highlighting this is a tax-deductible fee that is already subsidised by the government," he said.

"That is, the fee does not fully cover the cost to the government to administer the check.

"The nominal fee allows the government to fully subsidise the fee to volunteers, which is essential to ensure there is no financial deterrent to those who volunteer to work with children and vulnerable people."

Similar fees were applied by other states and territories operating registration systems, he said.

One advantage of the new system was that the checks were valid for three years even if an employee changed jobs or moved to another directorate.