Pakistan's Supreme Court on Tuesday suspended the government's extension of the term of office of army chief General Qamar Javed Bajwa, putting it on a possible collision course with the powerful military.

Prime Minister Imran Khan's cabinet later issued a notification reaffirming the extension, saying it had amended certain rules to tackle the court's objections.

"It is the prime minister's discretion to decide whether there is a need to grant an extension to a services chief in unusual circumstances," acting government spokesman Shafqat Mahmood told a news conference.

Under Pakistan's constitution, the army chief of staff usually serves a three-year term. Since the role was established in 1972, only one general has had his term extended by a civilian government.

However, Bajwa was handed a rare three-year extension on Aug. 19 with Khan's office citing increased tensions with neighbouring India over the disputed territory of Kashmir.

In a hearing to validate the extension on Tuesday, Chief Justice Asif Saeed Khosa said the court was suspending the cabinet's decision until the army produced detailed arguments on the reasoning behind the move.

"If the (regional security) situation is so then the army as a whole body can deal with the situation, not the individual," Khosa said. "If this criteria is allowed than every individual in the army can demand an extension on the same grounds."

He also said Khan's office has failed to follow procedure by submitting the extension request itself, rather than going through the office of Pakistan's president.

If the extension is blocked by the court, Bajwa's term will end on Friday. Khosa issued notice for representatives of the military and the government to appear in court on Wednesday.

During Bajwa's tenure the military has been accused by opposition politicians of electoral manipulation that helped Khan to power last year. The military has always denied interfering in politics.

Khan's administration has enjoyed good relations with the military, in contrast to tensions under the previous government of Nawaz Sharif.

The court's action surprised analysts tracking the influential military, which has ruled Pakistan for nearly half its 72-year history and takes the lead in setting security and foreign policy, and it came a day after several high-ranking generals were transferred to new roles.

"The unhappiness in the various institutions at the informal power that the army chief has acquired...may have brought different institutional forces together to challenge the extension," said Ayesha Siddiqua, an analyst who wrote a best-selling book on Pakistan's military.