The council says that it uncovered applications which ‘don’t appear to be genuine’ while carrying out financial checks.
Lincolnshire Police are now investigating, but no arrests have been made yet.
The money was claimed from several grant schemes including the Business Recovery Fund, which was developed to support businesses directly impacted by Covid and unable to fully trade.
They must have not benefited from other Government Covid support schemes.
The scheme was open to businesses with less than 50 employees.
Lincolnshire County Council distributed the grants to small businesses, with eligible ones entitled to between £2,500 and £10,000.
It is understood that councils were urged to verify grants by the government in a bid to cut down on waste.
Gary Douglas, principal investigator at the county council, said: “We take the misuse of public funds very seriously and it’s important to us that every penny is spent to the best effect.
"When we administered our grant schemes last year, we ensured there was a robust financial checking and referral system in place.
“Through this, we highlighted applications to a number of grant schemes that don’t appear to be genuine and we have referred these to Lincolnshire Police for further investigation.”
The details of the fraud were revealed in an annual report which went before the council’s Audit Committee on Monday.
“In 2021/22 we undertook validation of applications submitted for Business Recovery Fund grants being offered to small businesses.
"As a result, we identified a large fraud in excess of £300,000,” it says.
“This is currently being investigated by Lincolnshire Police and as part of our work has led to investigations of grant fraud in other counties.”
A spokesperson for Lincolnshire Police said: “We can confirm we are investigating reports of alleged fraud which involve grant applications via Lincolnshire County Council.
"The investigation is ongoing.
"No arrests have been made at this stage.”