Stockton Heath, Appleton and Lymm parish councils have all lodged objections to the proposals put forward by Warrington Borough Council.
Car parks affected are The Forge, at Stockton Heath and Pepper Street, Davies Way and Henry Street at Lymm.
Most contentious proposal is to cut the current two-hour free period at The Forge and Pepper Street pay-and-display car parks to one hour. A 50p charge would be introduced for the second hour.
Davies Way and Henry Street are currently free but would become pay-and-display - also with a one hour free period.
Stockton Heath council supports a "no return" restriction to stop motorists abusing the system by replacing tickets every two hours.
But they object to the reduced free parking period, pointing out that village shops have to compete with nearby supermarkets offering free parking.
They warn the changes will result in increased on-street parking which already causes problems in residential areas.
The council would support modest increases in charges in parking for three hours or longer rather than a reduction in the free parking period.
Similar objections have come from Appleton Parish Council, who point out the changes will hit shoppers and, as a result, retailers.
Lymm council also wants to keep the two-hour free period and is also opposed to ending free parking at Davies Way.
Shopkeepers and residents are also organising protests against the proposed changes which would be introduced in the autumn.