"I am a commando and I love my homeland. I will come back in a few weeks or months," Musharraf was quoted as saying by the Dawn.
Musharraf boarded an Emirates flight bound for Dubai that departed from Karachi airport at 3.55 am (0425 IST), a media report said.
"He was the last person to be embarked on the plane and then the gate was closed. The retired general appeared relaxed," the report said.
Musharraf, 72, has been facing treason trial since 2013 and he was barred from leaving the country in 2014 by the government. The order was declared as illegal by the Sindh High Court in the same year.
Interior minister Nisar Ali Khan yesterday told a press briefing that after consultation the government decided to let Musharraf leave the country for treatment.
He said Musharraf's lawyers had formally asked the government to allow him to undertake foreign travels.
"The government has decided to allow Musharraf to travel abroad for treatment. He has also committed he will face all cases against him in court," Khan said.
He was indicted in April, 2014 but since then no progress has been made in the case for various reasons.
Musharraf's All Pakistan Muslim League said yesterday that Musharraf was having problem in the backbone and he needed to go to the UAE to see a doctor.
It is believed that the decision to let Musharraf go out of the country will help heal a rift between the powerful army and the government, as the former was unhappy over treason trial of the former chief of army staff.
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