"Whatever happened to Chief Secretary (Anshu Prakash)... I say they should be beaten up, they should be thrashed... whoever obstructs the work being done for the common man, should be meted out the same treatment," Mr Balyan, a legislator from Uttam Nagar, said at a rally on Friday.
Mr Balyan later said he was misquoted, and he only meant that the public had the right to beat up officials who don't perform their duties.
"My contention was that the people should be given ration on the basis of their ration cards and that people have the right to beat up officials obstructing its implementation," he said.
The First Information Report or FIR was filed on Saturday with Dabri police station in west Delhi.
The comment came days after Chief Secretary Anshu Prakash alleged that he was beaten up by AAP legislators Amanatullah Khan and Prakash Jarwal in the presence of Chief Minister Arvind Kejriwal at the chief minister's home on Monday night, where he had been called for an emergency meeting.