Last month, the National Organisation for Tobacco Eradication (NOTE) asked the 42-year-old star to explain his actions after he was spied smoking at a cricket match in Mumbai and at a media conference in Delhi.
"This is not how a superstar should behave... Adored by millions (he) cannot lend a helping hand to promote smoking," the group's general secretary Shekhar Salkar said.
"We will be filing a case against him at the local court," Salkar said.
Anyone breaking the law faces a fine of 200 rupees (4.50 dollars).
The controversy comes as the muscled star rides high on the success of his newly released song-and-dance movie "Om Shanti Om", a movie about reincarnation.
The anti-smoking group filed a legal notice against Khan last month accusing him of breaking India's anti-smoking law banning smoking in public places.
The group called his smoking "illegal, indecent and unethical" and gave him 15 days to explain his actions that it said were seen on television by millions, including children.
The star's lawyers rejected the allegations, arguing Khan was smoking on both occasions in private places.
"A space where the general public does not have any access is excluded from the definition of a public place," Khan's lawyer said, according to the Calcutta Telegraph newspaper.
The anti-tobacco group said it was "disheartened" by Khan's response and said legal proceedings would be launched.
The government outlawed smoking in public places and the advertising of tobacco products in 2004 in a bid to stem rampant tobacco deaths.

Copyright AFP (Agence France-Presse), 2007