Bernd Hildenbrand was removed from his post in April on charges of causing the flag carrier millions of dollars due to corruption.
He was also put on the Exit Control List and barred from leaving the country as the government ordered the Federal Investigation Agency to hold investigations into the charges against him.
However, the Ministry of Interior in May granted him a special one-time permission to fly abroad for 30 days.
Hildenbrand is accused of leasing a plane from Sri Lankan Airlines for PIA use at inflated rates and at a cost more than the prevailing market rates.
He is also charged with selling a flight-worthy aircraft (A-310) of the airlines to a German museum at a throwaway price.
According to sources, Hildenbrand was given exemption to leave Pakistan because of alleged diplomatic pressure and he had given assurance that he would come back and face the corruption charges.