The CRB wants to reduce registrations in order to improve the efficiency of its services and cut costs, and introduce an annual registration fee to replace its current one-off fee.
It has not yet said how many checks charities will have to request annually in order for them to stay registered.
Mark Favager, head of communications at the CRB, said: "We will always be there to help those that are not registered."
But the NCVO said it would press the Government to fund a new network of organisations to perform checks on charities' staff and volunteers if the CRB excluded too many charities.
A number of umbrella-registered bodies already exist to obtain CRB information on behalf of non-CRB registered organisations. These can be local authorities, private companies or voluntary organisations. But the NCVO says many charities cannot afford their services.
Pete Moorey, parliamentary officer at the NCVO, said: "The only way to keep these checks absolutely free for those who won't be able to register with the CRB themselves is to have government-funded bodies. We would be amazed if the Government did not provide such funding in the Year of the Volunteer and of the Russell Commission. But first we need to know precisely what the CRB's plans are."