However, the Home Office, which has responsibility for the Criminal Records Bureau, has questioned the validity of the estimate.
It said it is unable to make public its own estimates of the cost to the sector, but challenged NCVO's calculations, even though they are based on Home Office figures for the number of checks likely to be requested over the next year by the sector.
"All the presumptions are correct in themselves, so the calculation is technically correct," said a Home Office spokesman. "But how accurate it is to multiply so many estimates together is another question. It just makes it all into a bit of a guess."
The fee increase, which will see the charge for standard police checks doubled from £12 to £24 and the more detailed enhanced checks rising from £12 to £29, was announced last month. The new rates came into effect on 1 July and are intended to ensure that the Criminal Records Bureau can become self-funding in the medium term.
NCVO is also concerned that the increases may breach the Compact agreement regulating the Government's relationship with the sector. "We believe that introducing such a fee rise without either consultation or an assessment of the impact is a serious breach of the Compact," said Richard Hebditch, Compact advocacy officer at NCVO.
Many charities, including NCH, Barnardo's and the NSPCC, have already voiced concerns for a lack of consultation.