QK Cold Stores (Marston) Ltd was prosecuted by South Kesteven District Council after the incident in June.
Grantham magistrates heard the employee was walking towards a freezer room in the warehouse's main bay when it happened.
The man equired skin grafts to repair the damage to his right leg.
At a hearing on Thursday, the court was told the council's environmental health team found no rear beacon on the forklift truck and a broken light.
It was also unclear whether the driver had sounded the horn, as required.
For the company, Phil Cookson entered guilty pleas to offences under the Health and Safety at Work Act 1974.
In mitigation, he said the firm had evaluated its risk assessment and since the incident had made £75,000 worth of improvements in the warehouse, including creating new pedestrian walkways for staff to avoid areas used by forklifts.
A firm has been fined almost £14,000 after a fork lift truck reversed over a man's leg in a warehouse, ripping his skin to the bone.