Musharraf, 72, is 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.
Yesterday, the Supreme Court upheld the decision of the Sindh high court, rejecting the appeal of the government. But it did not stop the federal government from putting new bars on Musharraf's foreign tours.
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.
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He was referring to several cases faced by Musharraf including the high treason charged in a special court for suspending the constitution in 2007, which has been declared under Article 6 as being punishable by death.
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 heel a rift between the powerful army and the government, as the former was unhappy over treason trial of the former chief of army staff.
Musharraf came to power in a bloodless coup in 1999, deposing then prime minister Nawaz Sharif. Facing impeachment following elections in 2008, Musharraf was forced to resign as president and went into self-imposed exile in Dubai.