A briefing on the bill said that while most police services were provided for the benefit of the public, there was a degree of private benefit for the users of the vetting service.
Mrs Tolley said: "Demand for police vetting has almost doubled in the past decade, and staff have had to fit this around their core policing duties."
New Zealand was one of the few countries in which police did not charge for security screening. Mrs Tolley noted that criminal checks in Australia cost between $52 and $60.
Some organisations could be exempted from the charges, such as volunteers working with children or family support services, or community organisations with small budgets.
The legislation said the fee would have to be fair and could only be used to cover the cost of the service.
The charges were expected to raise $2.2 million each year, which would be used to "deliver a dedicated, more efficient and sustainable vetting service".
Police were expecting to face greater demand for their services once the Vulnerable Children's Bill passed into law.
The bill will require any person who works with children to be vetted - up to 376,000 people.
Budget 2014 allocated $33.7 million to Child, Youth and Family, part of which was to carry out the new requirements in the bill. The police budget has not been increased in five years, and was cut by $45 million in last week's Budget.
Police processed around 500,000 checks a year, and 12,000 agencies were registered to use its service.
The Sensible Sentencing Trust said it was "incensed" at the plan for new fees. Spokeswoman Ruth Money said the charge would lead to fewer criminal checks and as a result, greater risks to the public.
The changes followed a review of police's cost recovery in 2012.
