In January a court in the northwestern state of Rajasthan cleared the 51-year-old actor of two charges related to the illegal use of firearms citing a lack of evidence.
The charges date back to 1998 when Khan was accused of hunting black bucks, a rare native species of antelope, while shooting a film in Rajasthan.
But on Wednesday authorities in the state said they would appeal the court´s decision.
"The application has been admitted by the court and notice has been issued to Khan," public prosecutor Pokar Ram Bishnoi told AFP.
Khan, known for his tough guy roles in Hindi films, has accused the state´s forest department of framing him in the case.
The actor is one of the Indian movie industry´s biggest draws and has starred in more than 100 films and television shows.
Last year his movie "Sultan", in which he played an ageing wrestler, smashed Bollywood´s box office records.
But he is no stranger to controversy and in 2015 he was cleared in another long-running case of killing a homeless man in a hit-and-run crash.
That decision is now being challenged in the Supreme Court.