Chief Judicial Magistrate M.Nazir Ahamed rejected the bail application of Senthil after the public prosecutor strongly objected to granting the bail.
The case has been posted for hearing on April 13.
Senthil was arrested along with former Agriculture Minister Agri Krishnamurthy in connection with the case on April 4.
On February 20, Muthukurmarasamy allegedly jumped in front of a train and was killed.
The case was transferred from the Railway police to the CB-CID which registered cases against the duo under various sections of IPC. Both were produced before the magistrate who remanded them in custody till April 17.