Gurmeet Singh Jolly, who goes by the name Shera, allegedly hit the waiter with the butt of a pistol during a verbal tiff at a bar in India's financial capital, Mumbai.
Police charged Shera with assault after receiving a complaint from the victim who sustained injuries, police said.
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"Shera has been charged... for possession of weapons and hitting the victim with a baton and the butt of a pistol before fleeing the spot," Mumbai Police spokesperson Ashok Dudhe said.
Shera has worked with Khan for nearly 20 years and is known to be a close confidante of the superstar, who is himself embroiled in a string of legal cases.
Although Khan was cleared last year of killing a homeless man in a late-night hit-and-run crash in 2002, that decision is now being challenged in the Supreme Court.
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