Police officials arrested the 69-year-old former military strongman this morning and took him to the court of judicial magistrate Muhammad Abbas Shah.
After hearing arguments by Musharraf's lawyer and the counsel of several persons who have filed petitions against him, the magistrate sent the former army chief on "transit remand" for two days.
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Musharraf can appeal in the Supreme Court against the magistrate's order.
The arrest came a day after the Islamabad High Court revoked Musharraf's bail for not cooperating with police officials investigating a case registered against him for detaining 60 judges, including Supreme Court Chief Justice Iftikhar Chaudhry, during the emergency.
Footage on television showed Musharraf being led into the magistrate's small and dimly-lit office by dozens of policemen and paramilitary personnel.
Musharraf looked shaken and was wearing a waistcoat over a shalwar-kameez.
He was also seen emerging from the magistrate's office and heading for his car. Musharraf waited in his car for some time as the magistrate initially reserved his decision.
However, he was driven to his farmhouse by his security detail before the magistrate issued the order for his detention shortly after 9.15 am.
Officials said Musharraf would be detained at his farmhouse at Chak Shahzad on the outskirts of Islamabad as he faced threats to his life and could not be sent to prison.
Earlier, police officials informed the magistrate that they did not need physical custody of Musharraf and he could be placed in judicial custody.
However, the lawyers of those who had filed petitions against Musharraf for imposing emergency in 2007 and detaining over 60 members of the superior judiciary contended that he should kept in police custody.
They also questioned why Musharraf had not been handcuffed by police after his arrest.
Musharraf's lawyer Qamar Afzal argued that his client should be kept in judicial custody as there were serious threats to his life.
Sources told PTI that authorities had asked for Musharraf to be placed in judicial custody as this would allow the administration of Islamabad to declare his farmhouse at Chak Shahzad a 'sub-jail' and detain him there.
Authorities have been focussing on this measure as officials are not keen on holding Musharraf at a jail due to threats to his life.
However, immediately after Justice Shaukat Aziz Siddiqui revoked his pre-arrest bail yesterday and ordered police to detain him, Musharraf and his security detail fled from the Islamabad High Court complex and drove to his farmhouse.
Musharraf's lawyers could not file an appeal in the Supreme Court yesterday as they were unable to complete certain formalities before the court closed for the day.
Analysts said Musharraf's arrest 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 clamped emergency rule six years back.
Musharraf has had to grapple with numerous legal problems since he returned to the country last month after nearly four years in self-exile.
Earlier this week, Musharraf was disqualified from contesting next month's general election, effectively ending his ambitions for a political comeback.
Authorities have also barred him from travelling out of Pakistan.
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