Aamir allegedly used a chinkara for shooting the movie in 2000 in Jam Kunaria village in Kutch, 375 km from here.
According to a forest department official, Khan and Reena, the executive producer of "Lagaan" and the actor's former wife replied to the notice issued last month and in return posed questions on issuance of the same.
"In their reply they inquired on what basis the notice had been issued to them. The film star is communicating through his advocate, but he will have to come here personally to get his statement recorded," the Conservator of Forest of Kutch Circle, R.L. Meena, told.
"After getting reply of our earlier notice, we have issued another notice to the executive producer to make clarification on specific issues," he added.
In the second notice issued to the film producer this week, the forest department posed queries regarding the shooting of chinkara, a protected species, without permission, the place where it was shot and how come the animal was shown unconscious.
"If the animal was actually unconscious, they will have to explain how it became so. This is very serious," said Meena.
Since the case is grave, the department "won't act in a hurry and is careful before going further", he added.
The forest officials are planning to file a case against the filmstar along with Reena and his present wife Kiran Rao for violating the law by capturing footage of the animal without permission. Reena was the executive producer and Kiran Rao was the assistant director of the film.
According to a forest official, Aamir had asked for permission to shoot the animal, but the request was turned down. Still, when the film was exhibited, there was a shot of a chinkara.
The forest department had earlier reportedly carried some preliminary investigation and the matter was closed.
But the case reopened when an environment group, Gir Youth Nature Club, registered a complained in July this year, just after the state criminal investigation department was asked to re-investigate poaching charges levelled against another Bollywood star Salman Khan, eight years ago during the shooting of the film "Hum Dil De Chuke Sanam".