The complaint filed two days ago before the Kozhikode Police Commissioner, is against the Vice Chancellor of Kerala University, Calicut Medical college Principal and three others.
A Peta release said a video footage released by a Malayalam TV channel recently had showed that a gardener, Vishwanathan, forcefully yanking guinea pigs by their ears from baskets and striking them on the head with a stick.
"We're calling on the police to help put an end to these atrocities and hold all guilty parties accountable," Koduri said.
The Ministry of Environment and Forests (MoEF) in January 2012 ordered that all medical and pharmaceutical programmes replace the use of animals with non-animal methods.
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PETA India has also asked the Committee for the Purpose of Control and Supervision of Experimentation on Animals to cancel the college's registration to use animals should the allegations be confirmed, the release said.
The Prevention of Cruelty to Animals Act, 1960, states that it is illegal "if any person beats, kicks, over-rides, over-drives, over-loads, tortures or otherwise treats any animal so as to subject it to unnecessary pain or suffering or causes, or being the owner permits, any animal to be so treated".
The CMC has to revise its curriculum, PETA said.
Those named in the complaint are K Mohandas,Vice Chancellor of Kerala University of Health Sciences, Ravindran, Principal, Calicut Medical College; Dr Jean Maliekkal, Head of physiology, Dr Narayana, Head of Pharmacology and Viswanathan.