Doncaster Council took action to close Nudge’s General Store & Off Licence in Simpson Place, Mexborough, in August after officers found vermin throughout the shop, kitchen and cellar.
Shop owner Paul Nagy, 51, said he spent up to £500 on pest control measures in the weeks leading up to the visit and asked the council for help.
But he claimed an officer in the authority’s environmental health department refused to help him.
He said: “I told them that I had dogs in, set traps and other pest controls but the rats were still there.
“They said there was nothing they would be able to do to help me.
“A couple of weeks later environmental officers were at my door and shut me down.”
He added: “I admit there was a problem but I was trying to sort it out and the council didn’t want to help me.
“I think they wanted to shut me down because they see my shop as a problem and want rid of it.
“I also expect that I will receive a fine at some point if they take me to court.”
“I have been here 25 years and now this closure has ruined my reputation.”
Mr Nagy said the shop is still shut and he has lost about £10, 000 worth of business because of the three months closure, while three of his shop assistants have also been without work.
He accepted pest control officers from the council are now helping him to clear the rats problem and he hopes to reopen soon.
But he added: “It is too little, too late. If they had helped me in the first place I may never have needed to shut down at all.
“The problem came from the front door not being closed properly and then the rats were getting in under the metal shutters.”
A spokesman for Doncaster Council said the authority was unable to comment publicly on the matter for legal reasons.
He said: “An investigation is ongoing and a prosecution may be brought.”