Kathiravan was killed by a suspected 10-member gang near his house at K K Nagar here with sharp-edged weapons, police said, adding the motive for the murder was yet to be ascertained.
Sankararaman, the manager of the Varadarajaperumal Temple at Kancheepuram, was allegedly murdered on its premises on September 3, 2004.
The two seers have been charged under sections 120-B (Criminal conspiracy) and 302 (murder) of the IPC.
The trial in the case was shifted to Puducherry from Chengalpattu by an order of the Supreme Court on a petition Jayendra had filed before it on October 25, 2005.