The top court dismissed the petition of Lt Col Samuel Kamalesan, who argued his Christian faith prevented him from entering a temple sanctum.
A bench led by Chief Justice Surya Kant held that refusal to obey a lawful command from superiors amounts to indiscipline, especially in a disciplined force.
The ruling emphasises that religious freedom cannot override professional obligations in the armed forces, and precedents show military discipline may limit individual faith-based exemptions.