In it, Mr. Chaudhry noted that his court’s paramount authority was enshrined in the Constitution. “Gone are the days when stability and security of the country was defined in terms of number of missiles and tanks as a manifestation of hard power available at the disposal of the state,” he added — a pointed reference to the military, which has ruled Pakistan directly for just under half of the country’s 65-year history, and indirectly much of the rest of the time.

The tussle between the military and judiciary has, for now at least, eclipsed the more traditional struggle between Pakistan’s civilian and military leaders. Analysts said it was unlikely to lead to a direct military coup but, with elections due to take place by next spring, it pushed the fluctuating dynamic between Pakistan’s power brokers in a new direction.

“Kayani is seeking to establish red lines for the activist Supreme Court.” said Arif Rafiq, an adjunct scholar at the Middle East Institute, based in Washington. “The army has historically seen itself as the guardian of Pakistan’s stability and as a cleansing force in politics. The Supreme Court has in many ways usurped that role.”

The tension appeared to stem from a long-running court case involving some of the country’s most senior retired generals. Last month, the Supreme Court ordered the government to begin criminal proceedings against former army and spy chiefs in an election-rigging case that dated to the 1990s. During the hearings, Gen. Aslam Beg, a former army chief, and Lt. Gen. Asad Durrani, a former chief of the powerful Inter-Services Intelligence Directorate, were accused of distributing public money to an alliance of right-wing political parties that opposed Benazir Bhutto’s Pakistan Peoples Party.

At least nine retired generals are facing judicial scrutiny for financial irregularities in different cases. The court has also put pressure on military intelligence agencies in the cases of “enforced disappearances” — the illegal abduction, torture and sometimes extrajudicial execution of suspected militants and nationalist rebels, especially in the restive southwestern Baluchistan Province.