The $8.50 fee would be waived for an agency that made 20 or fewer vetting requests a year, those facing extreme hardship, and registered charities.
Ms Collins said the cost recovery legislation would bring NZ Police into line with its overseas counterparts.
NZEI board member and Merivale School principal Jan Tinetti said she frequently used the police vetting service, including on at least 10 occasions last term.
Mrs Tinetti said a school such as hers would be hit hard because she did not have the flexibility in her "very tight budget" to divert funds from other areas to pay for this vital service.
"We don't have a choice, we have to do this as there is a legal requirement on schools to be really vigilant because we're in charge of vulnerable children. But every dollar counts when it comes to us paying the bills."
Mrs Tinetti said she hoped the Ministry of Education could come to the party.
Dane Robertson, president of Western Bay of Plenty Principals Association said: "It's a bill that should never even be seen by schools and should go straight to the Ministry of Education."
Mr Robertson said many schools would probably do fewer than 20 vetting checks a year but some larger schools would do more, and the costs would mount up.
Rotorua Lakes High School principal Bruce Walker applauded the intent of the Vulnerable Children's Act but in reality the police vetting process was "chaotic".
Mr Walker said rather than taking the usual three to four weeks it now could take months, and planning for events such as school camps could not be finalised without this information. Mr Walker said if the demand for this service had grown to the extent suggested then the Government should look at funding the extra resources needed by police.
Rotorua's John Paul College principal Patrick Walsh agreed.
Mr Walsh said increasingly schools were required to do these checks for coaches and managers of sports teams, and in some cases parents who billeted students in their home.
At the end of the day it was in the public's best interest, and the Government should come to the party, he said.
NZ Police vetting checks
• Demand grown by more than 100,000 since 2012/13
• Police asked to vet more than half a million people a year
• The $8.50 fee means police can recover more than $3m a year
Source: Police Minister Judith Collins