"We filed a complaint Nov 18 in Amber police station as there have been cases of cruelty on animals during the shooting of the film," Naresh Kumar Kadiyan, the chairman of the Haryana-based People for Animals (PFA), told.
Said Raghuraj Singh, station house officer of the police station: "We are looking into the complaint."
PFA has also filed a public interest litigation on this issue in the Rajasthan high court.
The charge of torturing animals is not new to the film's unit. The Society for Prevention of Cruelty to Animals had only last week sent a notice to Gowarikar's production company on the same count.
Shooting for the film featuring Aishwarya Rai and Hrithik Roshan in title roles has been going on here for a fortnight.
Animal rights activists are angry over the use of over 80 elephants, 100 horses and 55 camels for the shooting, alleging the animals are not treated well.
"These animals are being subjected to great hardships during the shooting and there is no facility of a vet doctor," Kadiyan said.
He added that the animals were forced to perform painful tricks using cruel methods. "These animals, fully decked up, are made to stand up long hours in the hot sun," he added.
The Rajput community is also unhappy with the film - but for a different reason.
Karni Sena, a Rajput community group, has alleged that Gowarikar was tampering with history. Rajput leaders have threatened to move court to stop the shooting.
The historical film depicts the love story of Mughal emperor Akbar and his Rajput wife Jodha Bai.
Coming from the maker of Oscar-nominated "Lagaan" and critically acclaimed "Swades", "Jodha-Akbar" is one of the most eagerly awaited Bollywood films.