He sought the report after the issue was highlighted in the local media.
Transsexuals Poorna and Ayesha were admitted in General Hospital in Ernakulam following injuries they suffered from alleged police brutality.
Poorna alleged that she was attacked while she was waiting for her mother at the bus shelter last night.
Ayesha, who rushed to the spot, questioned the police following which she also experienced police violence, they alleged.
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City police, however, said a section of police was deployed at Valanjambalam area following complaints from locals about the "problems" being created by transsexuals at night.
A policeman was attacked when heintervened to prevent them from disturbing public at busy area in Valanjambalam, police said.
Behera said city police commissioner has launched an investigation into the matter.
"Strong action would be taken if police are found guilty," he said.