Chief minister Oommen Chandy dismissed the CPI(M) charge.
A special investigation team arrested Mani from his house in Idukki district in central Kerala after he did not turn up for a polygraph test in connection with the murder of an Indian National Trade Union Congress leader 30 years ago. He had declined to comply, arguing the test was not legally maintainable.
A local court remanded Mani in judicial custody till December 4. Police registered three murder cases against Mani after he said at a public rally at Thodupuzha (Idukki) in May that the CPI(M) had often resorted to political killings.
He had also warned that rebel Marxist leader TP Chandrasekhran's murder (on May 4) was not the last.
"We had prepared a list of 13 and killed the first three. The first one was shot, the second beaten to death and the third hacked," he had added.
Soon after, the CPI(M) removed Mani from the Idukki district secretary's post, but found it difficult to abandon him altogether.