The Sindh High Court refused to remove his name from the Exit Control List (ECL) and advised 70-year-old Musharraf's advocate to refer the matter to the government.
The government had barred Musharraf from leaving Pakistan after he was arrested for his alleged involvement in three criminal cases, including the murder of former Prime Minister Benazir Bhutto.
The former military ruler had later received bail in all the cases. However, his name was not removed from the Interior Ministry's ECL that bars him from travelling abroad.
The Attorney General today said that Musharraf's name was put on the list because of criminal cases against him and the petition should be disposed off.
Musharraf, also an accused in the murder of Balochistan nationalist leader Akbar Bugti, has also been charged for committing high treason for abrogating Pakistan's Constitution during his 1999-2008 rule. He had imposed emergency rule in November 2007 and suspended the constitution.