A government move to speed up the planning process for shale gas drilling would reduce public confidence in the system, according to the county council.
It comes as ministers have proposed giving permitted development rights for shale gas exploration across the UK.
The government wants to make the decision-making process for the exploration stage of developments quicker.
Exploring for gas means operators would drill a well at a site and test for energy before carrying out further drilling.
Public interest in the shale industry has been high following concerns over fracking in Lancashire and North Yorkshire.
In a consultation sent out to local authorities, the Ministry for Housing, Communities and Local Government said the country needs to reap the benefits of shale gas for energy and create economic benefits both locally and nationally.
The move would mean that developers looking to drill for shale gas would not need to submit a formal planning application to the local authority.
Instead, the development would be approved at a national level to prevent delays.
The government said giving shale gas drilling a permitted development right would make the process simpler and quicker.
But, Lincolnshire County Council is expected to disagree with the proposal and say that such a plan would reduce “confidence in the planning process” for local people.
A report which will go before the authority’s Environment and Economic Scrutiny Committee will recommend that the council respond to the consultation and disagree with the plan.
Councillor Colin Davie, executive member for economy and place at the county council, said that local authorities should make decisions on shale developments as they do with oil drilling.
“The recommendations to the scrutiny committee reflect that local residents and communities should have their say over whether applications for shale gas extraction should be granted,” he said.
“As local authorities oversee planning issues for traditional oil and gas extraction, they are best-placed to facilitate community involvement and ultimately take decisions for shale gas extraction too.”
The consultation comes as part of a series of measures outlined by the government on shale gas, including setting up a new regulator and introducing a local authority support fund for applications.
After announcing the plans, energy and clean growth minister, Claire Perry MP, said the measures would secure the country’s energy supply.
She said: “British shale gas has the potential to help lower bills and increase the security of the UK’s energy supply while creating high quality jobs in a cutting-edge sector.
“This package of measures delivers on our manifesto promise to support shale and it will ensure exploration happens in the most environmentally responsible way while making it easier for companies and local communities to work together.”