Kalimuthu, who hailed from Salem in Tamil Nadu, along with another man was handed over to police by locals two days ago.
There are reports that he was beaten up by police in custody following which he died.
Waynad SP K Karthick, who is in charge of the case, said an enquiry is on.
Demanding judicial probe into the man's death, Opposition leader Ramesh Chennithala said there has been a "serious lapse of rules and regulations and human rights violation".
"The man was taken into custody 48 hours ago and the police failed to follow rules and he was not produced in court also," he alleged.
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