Officials want meters removed from Metheringham station car park after complaints of parking chaos from residents.
Commuters dodging charges have been accused of clogging up nearby streets.
East Midlands Trains has now brought in a £2 daily tariff at the station following a six-month stay of execution.
But residents are reporting problems because some motorists are boycotting the car park.
Chris Briggs, head of transportation at Lincolnshire County Council, is demanding action from East Midlands Trains.
"We have requested that the charging machines at the Metheringham station are removed," he said.
"We are concerned as we invested in improving the car park there to encourage people to travel by train by parking their cars for free."
Julie Hill, who lives in Pulman Close, said: "Now that the charges have been put back on we have once again had cars parking around here.
"Bin lorries are having a job getting round. The answer is simple – it should be free to park at the station."
Patricia Bradwell, county councillor for Billinghay and Metheringham, said she is disappointed at the lack of consultation from EMT.
"As a strategic partner of the county council, I would expect them to liaise with us out of courtesy rather than just implementing the charging," she said.
"This is causing an inconvenience to residents as they often cannot park outside their own homes.
"It is a shame that the enhancements that the council has made to the car park are now actually having an adverse effect and putting people off from using the train station."
But East Midlands Trains spokesman Emma Knight insisted that the issue had been discussed.
"We have been in liaison with the local council about the introduction of these charges and we actually delayed implementation of the charges for six months at the request of the council," she said.
"We do believe the car park offers good value at just £2 and we do know that rail passengers are continuing to use the facility."