Rath has been indicted along with former Military Secretary Lt Gen Avadesh Prakash in the over Rs 300-crore land scam case in Darjeeling.
A division bench comprising Justice Geeta Mittal asked Rath to approach the Armed Forces Tribunal to challenge the proceedings against him.
Justice Mittal said, "Jurisdiction of this court is barred by Armed Forces Tribunal Act. In view of this, the petition is dismissed with liberty to petitioner to approach the tribunal."
Rath had also challenged the government's decision to scrap his appointment as Deputy Chief of Army Staff in the backdrop of the alleged scam.