Musharraf, 69, appeared in court this morning for the extension of his interim bail in a case related to the sacking of over 60 judges during the 2007 emergency.
However, Justice Shaukat Aziz Siddiqui rejected his application and ordered police to arrest him.
Police tried to reach the former President but his security detail of army commandos rushed him out of the courtroom and escorted him to his black SUV.
Musharraf's motorcade drove out of the complex before police could act.
A large contingent of police and paramilitary personnel deployed at the complex to provide security to Musharraf also did not act as the former dictator's bodyguards pushed through a crowd of lawyers and bystanders.
Musharraf, who returned to Pakistan on March 24 after a nearly four-year long self-imposed exile abroad to contest the May 11 general elections, is currently holed up in his Chak Shahzad farmhouse on the outskirts of the federal capital.
If Musharraf is arrested, he would become the first former army chief to face such an action.
Analysts said this could put the judiciary in conflict with the powerful military, which would not like to see a former chief being humiliated or insulted in public.
The analysts further said that if Musharraf was put on trial, members of the current military leadership, including army chief Gen Ashfaq Parvez Kayani, could be dragged into the matter as they were part of Musharraf's inner circle when he imposed emergency rule in 2007.
In a message posted on Facebook, Musharraf's office said: "We expect this unwarranted judicial activism, seemingly motivated by personal vendettas since his return to Pakistan...will cease and the Supreme Court, without prejudice, will immediately grant necessary relief...the absence of which can result in unnecessary tension amongst the various pillars of state and possibly destabilise the country."
Sources told PTI that the government was considering a proposal to declare Musharraf's farmhouse a "sub-jail" so that he could be detained there.