The police had on Saturday filed an FIR against Major Shukla of 24 Rashtriya Rifles and more than 30 soldiers who raided the police station and launched an alleged attack on cops on Friday night.
Jammu and Kashmir DGP SP Vaid had lodged a strong protest with the corps commander Lt Gen JS Sandhu who ordered an inquiry.
"Efforts to create divide between Army & Police by anti- nationals won't work. We're together always working as brothers in arms," Lt Gen Sandhu said on the official Twitter handle of the Chinar Corps.
Eight policemen including an Assistant Sub Inspector were injured after dozens of armymen barged into a police station in Jammu and Kashmir's Ganderbal district and beat them up.
The injured policemen were taken to the hospital and an FIR was registered against the armymen for attacking a police station and thrashing policemen on duty.
The scuffle allegedly broke out after a team of armymen, who were not in uniform and were returning from the Amarnath Yatra, was stopped at a barricade in Gund by policemen as no pilgrims are allowed to travel at night.
Police said the armymen insisted on moving and thrashed the cops when they weren't allowed.
"We had informed the Commanding Officer of a nearby Army camp that these jawans be taken to his camp for the night," said a police officer.
"But suddenly troops stormed a police station in Gund, beat up cops," he added.
A defence spokesperson said measures had been taken to prevent the recurrence of such incidents.