Birdi, commanding officer of the 68 battalion BSF, was formally arrested by the state police after he was handed over to the special investigation team by BSF authorities.
A senior police official said, "We have arrested him and he will be questioned about the killing of 16-year old Zahid Farooq Sheikh."
On Feb 5, Sheikh died after being shot in the chest by a BSF trooper in Nishat area of the city.
The state police had earlier arrested a trooper, Lakhwinder Kumar, after an in-house enquiry by the BSF found him to be involved in the killing of the youth.
During the investigation, the trooper said that he had shot at the youth under orders from his commandant, Birdi.