Justice P S Teji issued notice to the whistleblower, referred to as Mr X in the petition, as the Central Forensic Science Laboratory (CFSL) at Hyderabad was not a party to these proceedings.
The CBI was seeking copies of the documents and the pen drive on the ground that it would help them in probing the case and verify the whistleblower's allegations of tampering.
Mr X had approached the court for protection from arrest and interrogation in the case. The high court in February last year had granted him the relief.
The court has listed the CBI's application for further hearing on July 11.
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During the arguments today, Mr X's counsel Badar Mehmood, opposed CBI's application, saying since the agency has given a clean chit to the accused in the case, why it was asking for the documents to be sent to CFSL.
A 40-member special investigation team of the CBI has been probing Vyapam-related irregularities since July last year on the Supreme Court's direction.
The agency is also probing some deaths - murders and suspicious suicides - in the state, which have been connected to Vyapam.