"That's a significant amount of extra money to find from an already stretched budget."
Sector Enablement and Support deputy secretary Katrina Casey said a recent survey of early learning services found they asked police to vet an average of six people a year.
"Some early learning services, like kindergartens, will be exempt, regardless of how many police vets they request, because they are registered charities," Ms Casey said.
But home-based learning services are not so fortunate.
Under the Vulnerable Children Act 2014 and Ministry of Education requirements, police checking for home-based services are required of anyone over the age of 17 years living in the carer's home.
A police spokesman said the decision to charge education providers for the checks stemmed from the growth of this service.
"With over 630,000 requests from up to 10,000 different agencies expected in 2017 alone, it puts considerable strain on police resources," the spokesman said.
"Legislation and regulation have been put in place to enable the police vetting service to recover actual and reasonable cost to ensure ongoing resourcing that is resilient to demand."
Ms Overton-Stuart said with government funding of early childhood education having received little increase over the past few years, it would mean the service had some hard calls to make on how to fund the extra cost.
"It's several thousand dollars that will need to come out of somewhere else - unless, of course, we get a funding increase from the government."
Ms Casey said analysis of vetting by the education sector last year found a number of unnecessary checks being requested and recommended vetting every three years.
But Ms Overton-Stuart said annual vetting was necessary because anything could change within a year.
"Of course, we believe vetting is necessary for the safety of the children in our care.
"It is non-negotiable that we will continue to use this service. That is just a one of the costs we have to ensure that we provide the best possible environment for the children in our care."