The district authority is being consulted on the proposal ahead of a final decision by Lincolnshire County Council.
Leo Group’s amended plans would see the four planned eco-homes become “affordable housing”.
Revised drawings and plans show the area without the community hub.
The proposals would also see the facility demolished and replaced with upgraded odour filters, further away from residents.
A community hub which was included in the original plans was removed in the resubmitted proposal.
The rest of the site would incorporate a fishing lake, walking and cycling paths.
But the council objected to the affordable housing contribution, as well as the impact on odour, air quality and noise.
Further concerns were raised about how the development would impact on transport and traffic and the authority suggested monitoring the number of heavy good vehicle movements.
Skellingthorpe Parish Council also maintained its objection to the plan.
Andrew Walshaw, of the parish authority, said the authority had concern over both noise and traffic.
“We strongly object against this,” he said.
“Everyone knows it as Smelly Skelly and it has been for many years. Our main concern is the traffic and it’s not just the amount, it’s the noise.
“We appreciate that it would be a modern plant, but our objection still remains the same.”
A final decision on whether the proposal is approved will be made by Lincolnshire County Council at a later date.
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