The problem has been around for years. But, no one seems to know where the flies come from.
Residents said a chicken farm was located quite a distance away from the 10-year-old food court.
Owing to poor management of the food court, operators have to replace broken tables and chairs on their own.
Razali Hamid, a 43-year-old customer, said he had to cover his drink with his palm to stop the flies from getting into his drink.
He said the authorities should improve the management of the food court.
He said it opened late into the night and was a popular eating spot among residents.
"I am amazed by the lack of attention given to the food court as it is at a strategic spot near the main road, residential area and a school," said Razali, adding that the local authorities should spruce up and beautify the surroundings.
Operators said the food court was infested with flies for about three months every year.
Tangkak Municipal Council health officer I.K. Raman said the damaged furniture and fans had already been repaired several times. He said continuous, and possibly careless use of the fans by the operators could have caused them to get damaged sooner than expected.
"The operators should clean up their spot before closing every day and not solely depend on the council. We merely provide the facilities. They should cooperate with us," said Raman.
"I suggest that the operators form an association so that any problems can be forwarded to us for action to be taken."
He said the operators should take a day off each month and inform the council so that the food court could be cleaned.
"I hope the operators will bear with the council which is under financial constraint and short of manpower.