Labour's community and voluntary sector spokeswoman Poto Williams said groups such as the Cancer Society would face charges for each criminal check unless they were exempted by the Police Commissioner.
"Registered not-for-profits should be able to keep this money and use it to do good in their communities," she said.
"Instead they are being used as a source of revenue for an underfunded police force."
The Cancer Society told the committee it needed to vet about 1500 people a year for volunteer jobs such as driving terminally-ill people to get treatment, and it would face new costs of around $10,500 unless it was exempted. Other organisations including Age Concern, the Teachers Council, the Salvation Army and the Blind Foundation expressed similar concerns.
The commissioner has been given powers to exempt organisations from the charge - expected to be $5 to $7 per check - but it is not clear what criteria will be used or who will be exempted.
Charities that submitted on the bill said charges should be waived if the organisation provided a public good, depended solely on donations and had large proportions of volunteer staff.
Police Minister Michael Woodhouse's office said he had no plans to make any changes with regard to waiving fees for charities.
"It has always been the intention to provide for exemptions," a spokeswoman said.
"However, the exemptions will occur through regulations, not through the Cost Recovery Bill which is an enabling legislation."
Labour MPs, in their report on the bill, said the law change could allow police to add new "user pays" charges for core services without the scrutiny and debate which came with legislative changes.
They said Search and Rescue could qualify as a "demand service" and could be charged for in future.
Ministers have previously said that cost recovery would only be applied to police vetting, and would not be quietly extended to other services at a later stage.
Charging for criminal checks was expected to raise $2.2 million a year.
