"CPI-M cannot expect to have their way by intimidating the investigating officers," Chandy told reporters after a cabinet meeting.
Earlier the practice was to name the accused by the party itself when any political murders took place, Chandy said, adding, that system has changed.
Police would register case on the basis of evidence they gather during the probe, Chandy said, rejecting CPI-M's charge that its party activists arrested in connection with the case were being tortured in police custody.
Chandy said there was no political motive in registering a case against CPI-M leader and former state minister Elamaram Kareem for allegedly threatening police officers. "Kareem has not denied the speech made by him", Chandy said.
Meanwhile, state Home Minister Thiruvanchoor Radhakrishnan said government would provide all support and protection to officials, investigating the Revolutionary Marxist Party (RMP) leader T P Chandrasekharan murder case.
"CPI(M) is trying to block investigation by threatening investigators and raising wild and false allegations against them. The government has the moral responsibility to protect law and order," he told reporters here.
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"The intention of CPI(M) leaders is just to politically harass the government and block the investigation," he said.
Quoting reports, the minister said Kareem had threatened a DYSP and a sub-inspector who are part of the team probing the murder.
Reacting to the case being registered against him, Kareem denied he had threatened the police official probing the murder case.