The accused, identified as 58-year-old Ajit Vadakayil, a retired captain of Merchant Navy, was arrested on Thursday, police said.
According to them, the actor had complained that "false messages" being circulated through electronic media, which claimed donations sought in his TV show were going to a trust working for a particular religion.
"Vadakayil was arrested and was immediately granted bail. Today, we filed a charge sheet against him in the court," a crime branch officer said.
Last month, Aamir Khan had met Joint Police Commissioner (Crime) Sadanand Date at Mumbai Police headquarters and briefed him about "false and malicious messages" being circulated on social networking sites Facebook, Twitter and Whatsapp were damaging his image and reputation of his issue-based reality show.
More From This Section
The Cyber Crime Investigation cell had later blocked the content on the website.
Khan, through a social networking site, had said false and malicious messages were circulating through various electronic media, including Whatsapp, Facebook, Twitter and other social media networks alleging donations are being sought in his television programme Satyameva Jayate, in relation to an entity by the name of Humanity Trust working for a particular religion.
The actor had also clarified "all donations sought in the show are used and channelised for entirely deserving and secular causes, contrary to the content of the highly mischievous/malicious insinuations in the messages, being circulated by vested and unscrupulous interest.