The criminal complaint was filed by Rajesh Kunte, Secretary of RSS unit at Bhiwandi, a powerloom town near here.
Addressing a rally at Sonale in Bhiwandi on March 6, Rahul had said, "RSS people killed Gandhiji."
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In his complaint to the court, Kunte said the remarks were defamatory and sought action against the Congress leader.
BJP has already moved the Election Commission against the Congress Vice President.
"I registered a criminal complaint against Rahul Gandhi with the First Class Magistrate Court at Bhiwandi. Through his speech, he has harmed the reputation of our organisation. The remarks were made with an ulterior motive," Kunte told PTI.
"His allegation, that RSS men killed Mahatma Gandhi, was against the judicial verdict in the case. This is a deliberate attempt for electoral gains," he alleged.
The court is likely to hear the matter on March 27.