Musharraf boarded an Emirates flight bound for Dubai that departed from Karachi airport at 3.55 am (2255 GMT) an airport source told AFP, adding the retired general appeared "relaxed".
"He was the last person to be embarked on the plane and then the gate was closed," the source said.
Musharraf free to fly away
A large convoy of police and paramilitary rangers left Musharraf's home in Karachi around 3:30 am as a decoy to waiting media crowding his street, while the general travelled to the airport separately.
Lawyers for the former president, who is facing multiple charges including treason and murder over the assassination of former prime minister Benazir Bhutto, have said he needs urgent medical treatment not available in Pakistan.
"I am going abroad for treatment but will return to face the cases against me," a party spokesman in Karachi quoted him as saying. "I am a commando. I love my motherland."
"Six to eight weeks are required for the treatment and then he would go back home," said Dr Amjad Malik, a spokesman for Musharraf's All Pakistan Muslim League party in Dubai.
Musharraf was banned from leaving Pakistan in March 2013 after he returned to the country on an ill-fated mission to contest elections. The former ruler was barred from taking part in the polls and instead faces a barrage of legal cases.
SC upholds SHC decision to remove Musharraf’s name from ECL
On Thursday, the government agreed to strike Musharraf's name off the no-fly list. A day earlier, the top court declared the ex-president could travel abroad.
“The government has decided to allow Musharraf to travel abroad for medical treatment. He [Musharraf] has also committed that he will face all cases against him in court,” the interior minister announced on Thursday at a news conference.
Chaudhry Nisar said the government was removing the retired general’s name from the Exit Control List (ECL) under the directives of the Supreme Court.
The former president’s lawyers have committed before the apex court that he will return to the country after four to six weeks, he added.
On Wednesday, the Supreme Court rejected the federal government’s two-year-old appeal against the Sindh High Court’s decision to remove Musharraf’s name from the ECL.
The former president reserved a seat with a foreign airline at 4:30am Thursday but the Federal Investigation Agency (FIA) intervened, saying he would not be allowed to travel unless the government removed his name from the no-fly list. The booking had to be cancelled.
“Today his lawyers moved a proper application for removing his name from the ECL, after which the government decided to allow him to go abroad for treatment following the apex court judgment,” Nisar said at the media briefing.
The minister added the detailed judgment on this case was not received but the decision to remove Musharraf’s name from the ECL was taken as per the apex court’s ruling.
Nisar said every decision had some motives but there was no confusion regarding the case against the former military ruler.
Govt challenges SHC’s decision to remove Musharraf’s name from ECL
Without taking its name, the interior minister criticised the Pakistan Peoples Party for censuring the government like if the government would lose the right to govern if Musharraf was allowed to go abroad.
“What did they do during their five-year tenure despite booking Musharraf over Benazir Bhutto’s murder?” Nisar questioned. “We initiated the treason case against him and opposed every move for removing his name from the ECL. Everyone including the government has to follow the verdict of Supreme Court.”
If the government, he added, is willing to allow Musharraf to travel abroad, it would not have filed appeals against the judgment of first the lower court and then the high court orders.
He also brushed aside speculation of any clandestine deals behind the decision to allow Musharraf to leave the country.
“The prime minister has no personal grudges against Musharraf and he has pardoned him for whatever he did with him,” Nisar clarified.
He added the government now did not put anyone’s name on the no-fly list. The powers have been delegated to the National Accountability Bureau, FIA and the defence headquarters.
Musharraf challenges his non-bailable arrest warrants
Musharraf’s name was put on the ECL after he returned to Pakistan in 2013, hoping to lead his party into the general elections.
He was, however, disqualified from contesting the polls and found himself fighting an array of charges relating to his time in power.
Musharraf was the army chief when he seized power in a coup in 1999. He was the president till 2008 when a democratically elected government came into power and ousted him. He left the country to live in self-imposed exile in Dubai and London.
The charges relate to the former general’s imposition of a state of emergency in November 2007 and the assassination of former PM Benazir Bhutto the same year. Musharraf, 72, denies all the charges and has termed them “politically motivated”.
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