While the Kerala Police have maintained that two Maoists were killed in a shootout in the forest, human rights activists have said that this was a "fake encounter".
Friends and relatives of the two prevailed upon the police to preserve the bodies till Monday evening.
According to the police, the Kerala Thunderbolts - - an elite commando force of the state police - - was on a patrol in the deep forests of Nilambur.
"It was they who fired first and the fire was returned, " said a top police official.
The two ultras were identified as Koppam Devarajan and Ajitha alias Kaveri.
Their bodies were brought to the Kozhikode Medical College hospital on Friday night and the autopsy was conducted on Saturday.
But on Saturday morning close relatives and friends of the two arrived at the hospital with a group of human rights activists, including Ayinoor 'GROW' Vasu and demanded justice, saying it was a "fake encounter".
"This was no encounter, instead it was a fake encounter and we demand a judicial probe into what happened, " said Vasu.
The police, finding it tough to pacify them, took them into custody.
They were let off two hours later.
Relatives of Devarajan, who included his aged mother, said they have had no contact with him for the past 30 years.
The Communist Party of India, the second biggest ally of the LDF government led by Pinarayi Vijayan, has lashed out at the manner in which the police action was conducted and condemned the incident.
State Congress President V. M. Sudheeran demanded a judicial probe into the entire episode and the Kerala State Human Rights Commission has directed the state police chief to conduct an enquiry and submit a report.