The case was registered against Elamaram Kareem, who is currently the CPI(M) state secretariat member.
CPI(M) activists led by Kareem had staged a protest march here on May 26 alleging that the SIT, probing the murder, was biased.
Some CPI(M) workers have been arrested in the case relating to the murder of Chandrasekharan, a Marxist rebel.
A case was registered the same day against Kareem and others for taking out the march without permission and obstructing vehicular traffic.
Reacting to the registration of fresh case against him, Kareem denied he had threatened the police official probing the murder case.
"I have not threatened anybody," he said.
Kareem said he had only brought to the attention of the people the "torture" of people taken into custody for interrogation in connection with the murder case.