The comments came amid strong speculations in Pakistan that Musharraf can leave the country under a deal with the government, Xinhua reported.
However, the interior minister said the former president's name is included in the Exit Control List and he can only leave the country if allowed by the country's apex court. "Musharraf's name was on Exit Control List and it would not be removed till the court's decision," Khan told reporters in the national capital Islamabad.
Speculations of Musharraf's leaving the country gripped Pakistan after he was granted bail in three criminal cases against him few days ago.
On Thursday, police formally arrested the former president in the murder case of a religious cleric, Abdul Rashid Ghazi, who was killed in a military raid on Islamabad's Red Mosque in 2007. Ghazi was among the 90 religious students, killed during the operation.
Musharraf was also charged in the murder case of the 2007 assassination of former prime minister Benazir Bhutto, the killing of a senior tribal elder Nawab Akbar Bugti in 2006 and placing top judges illegally under house arrest during his rule. He already got bail in two cases.
The former military ruler also faces high treason case and the government has formally approached the Supreme Court of Pakistan to start the trial.
Prime Minister Nawaz Sharif had himself declared to initiate high treason case against Musharraf for abrogating the constitution when he sacked his government in 1999 and later suspended the constitution in 2007 when he had imposed emergency rule.
The apex court had ordered the government to question Musharraf as to why he had dismissed an elected government and in what circumstances he had suspended the constitutions in 2007.
The interior minister said the Federal Investigation Agency has been directed to accelerate investigation into the treason case against the former president and would present the report as soon as possible.
He said the investigators have been directed to complete investigation in six weeks.