Judicial Magistrate Veluswamy passed the order on a petition by the CB-CID seeking ten-day custody of the two, arrested in October in connection with various cases including the Advani pipe bomb case and murder of BJP and Hindu outfit leaders in Tamil Nadu.
Earlier, Fakruddin and Malik told the magistrate that they were being tortured and they were innocent. They alleged police were planning to kill them in "encounter".
However, the duo claimed they had confessed under pressure from Police.
Granting seven days police custody, the magistrate directed the police to produce the two in the court on December 2. He also said police could allow their relatives and advocates to meet them.
Murugan was waylaid by a four-member gang which came on two motorcycles and hacked to death in broad day light.