After absconding for three years, Balamurugan had surrendered before the Madurai Judicial Magistrate and was lodged in the Central Prison here late last year.
Justice Kalyanasundram rejected the bail plea of Balamurugan.
Balamurugan and another person Nondi Mahalingam were arrested during police raids conducted following suspected movement of Naxalites in 2007 at Varushanaadu in Theni district.
They were released on bail and went missing three years ago.