The former cricketer-turned-politician's arrest has turbocharged what was already a tense showdown between the military and Khan's supporters. (Reuters)

Detained former Pakistan Prime Minister Imran Khan was due to appear in court on Friday, shortly after the Supreme Court of Pakistan ruled the arrest of Khan is unlawful and ordered his immediate release.

"Your arrest was invalid, so the whole process needs to be backtracked," Chief Justice Umar Ata Bandial told Khan at a hearing in the capital Islamabad on Thursday.

Khan was instructed to keep himself safe by being in the bench's custody under police guard until his Friday court appearance.

However, should Khan be released, the government has pledged to re-arrest him, which might lead to more unrest. Arrests should not take place on court premises, Bandial said Thursday.

Khan, 70, was ordered back to the same police headquarters where he has been sequestered for the past 48 hours on the condition it should be treated as a "residence".

However, interior minister Rana Sanaullah tersely stated authorities would re-arrest him. "If he gets bail from the High Court tomorrow, we will wait for the cancellation of bail and arrest him again," Sanaullah told Dunya TV.

Khan was taken into custody on Monday by authorities following a hearing on the Al-Qadir Trust case.

The former Premier's detention followed months of political crisis and came hours after the powerful military criticized the former PM for accusing a senior officer of being involved in a plot to assassinate him.

On Tuesday, Pakistan's authorities said Khan was facing an inquiry by the National Accountability Bureau in the Al-Qadir Trust case involving the PTI and a property Tycoon.

A deal struck between the two parties reportedly caused the loss of 50 billion Pakistani rupees ($17.6 million) to the national exchequer.

Nearly 1,000 people have been detained in Punjab since protests broke out following the arrest of Khan.

In a statement, the police reported the arrest of "945 lawbreakers and miscreants from across the province."

Local media reported at least eight people were killed and 290 were injured in light of the clashes.