The registration period for the scheme, which will see businesses with more than 10 parking spaces charged £279 a year for each space, is about to close.
Nottingham City Council said money from the scheme, which starts next April, would be invested in public transport.
Some companies have complained the charge punishes responsible employers.
Jane Urquhart, the city council’s head of transport, said she thought the 25% of companies which have failed to register may have been confused about the process or were unaware of the charge.
She said the council would be contacting the businesses over the next few months to find out why they had not signed up.
Firms which do not register could face fines and court action.
Andrew Jameson, managing director of Keltruck, a national firm which has a base at Riverside Industrial Estate, said he had registered for the charge but did not agree with it.
He estimated the scheme would cost his company £170,000 a year if it was extended nationwide.
He said: “As a responsible employer who provides off-road parking for my employees, I’m going to be penalised.
“The roads around Riverside Industrial Estate are lined with cars for other companies which don’t provide sufficient parking so there is a disparity.”
Ms Urquhart said the subsequent investment in public transport would benefit all businesses in the city in the long-term by helping to reduce congestion.