Attorney General Anwar-ul-Haq informed a three-judge bench headed by Chief Justice Iftikhar Chaudhry of the government's position while responding to a petition that had asked the apex court to restrain the civilian administration from taking any action against the army chief.
The petitioner had asked the court to direct the government not to take any steps against the army chief like the recent sacking of Defence Secretary (retired) Lt Gen Khalid Naeem Lodhi by Prime Minister Yousaf Raza Gilani.
The Chief Justice directed the Attorney General to seek instructions from the government and to file a reply on the matter in two weeks.
The Chief Justice further observed that the situation should "move towards an improvement".
The prime minister had recently sacked Lodhi, a confidant of the army chief, on charges of gross misconduct and creating misunderstandings between the government and the military.
Lodhi has challenged his dismissal in court, saying he was given no opportunity to explain his position.
Lodhi earned the premier's ire by filing an affidavit in the apex court that contended the government had no operational control of the army and ISI.
The affidavit was filed in a case related to the memo scandal that has triggered a simmering row between the government and the military.
The alleged memo had sought US help to stave off a feared military takeover in Pakistan after the killing of Osama bin Laden in May last year.