Charitable trusts would not be charged any fees, and they can be waived for organisations facing "extreme hardship" or in cases of exceptional circumstances.
However, Lynda Stuart, president of education union NZEI, said the vetting charge would be another additional cost on schools and in many cases a significant one.
"Principals, teachers and support staff fully support any measures that are going to keep our children safe. But schools and ECE services need more money to meet these extra costs.
"It is a considerable cost. There are only two areas you can get any flexibility from [to reduce costs] - and that's your support staff and cutting their hours, or your curriculum resources. Those are the only areas it can come from, and that directly impacts on children."
Some schools are already warning their community about the impending charges.
Tamahere Model Country School in Hamilton has sent a notice to parents asking them to visit the school office now if they planned to be involved with any camps or trips in the future, in order to avoid the charge later this year.
Principal Waveney Parker said she realised that didn't help police, but given the school from this year was screening all parents who volunteered for camps, as per best practice guidelines, the cost would be significant.
"Say if 40 parents need to be police vetted for camp, that's another $400 of cost that we haven't had in the past ... I understand it's costing the police right now but it's now going to cost us."
Parker said the school was considering if it was fair to ask parents to pay.
"Parents are already giving up their income for two or three days, they are paying petrol costs driving there and things like that, so it is possibly going to have to be worn by the school. We haven't quite crossed that bridge yet."
Police Minister Paula Bennett said New Zealand was joining the majority of countries in the world who allow vetting charges.
Since 2011/12 the number of vetting requests to police had increased 39 per cent to 550,000 in 2015/16.
"Police have been working hard to develop a process to recover some of the actual costs associated with the vetting service we provide - particular as demand has grown significantly in recent years.
"If an approved agency is facing exceptional financial hardship or exceptional circumstances, then it may be exempt from fees."
Labour, the Greens and NZ First voted against legislation that was passed in November to allow police to charge for vetting.
Labour's community and voluntary spokeswoman Poto Williams said all steps should be taken to ensure people working with children and the vulnerable were vetted by police, and making organisations pay for the service was counter-intuitive.
"The process of police vetting is really important to ensure that we keep vulnerable people safe, we think if you were going to put a charge on community groups and schools you were basically handing government money from one department to another."
Williams said the overseas examples showed vetting costs started out small but then increased over time to up to $50 or $70.
"It is an ongoing cost and one that we have no indication how much that might likely be."
Head of the Early Childhood Council, Peter Reynolds, said many ECE centres would need fewer than 20 police vets a year, and so would not pay any charges. For those that did, the cost would not be of major concern.
But Reynolds said a problem facing the sector was the time it took to have a person vetted - an average of 20 days. That caused major problems when hiring staff and the council was working with the Ministry of Education to try to get the processing time cut to around five working days.
The law change will allow Police to recover more than $3 million each year. The vetting service provides criminal history checks and other relevant information of potential employees and volunteers to approved agencies that provide care to children or vulnerable members of society.
Criminal checks are also provided for overseas visas and work permits.
