The case was re-opened in the wake of Mani's controversial speech in which he stated his party had in the past drew up a list of some political foes to be eliminated and executed it.
Judge K Ramakrishnan turned down Mani's plea considering the prosecution argument that the investigation in the case would be affected if Mani was released on bail.
The court refused bail to two others also in the case and extended their remand period till December 31.
Mani was arrested and remanded to judicial custody on November 21 and sent to sub jail in Peerumade in Idukki district in connection with murder of INTUC worker Anjeri Baby.
Police had registered a criminal case against Mani and two other party activists by re-opening the murder of INTUC activist, Anjery Baby, 30 years ago.