Musharraf had announced last week that he intends to return to Pakistan a week after the installation of the interim administration to lead his party in the polls.
The Pakistan Peoples Party-led government will complete its term on March 16 and the caretaker set-up is expected to be formed the same day.
Ali told the media that the anti-terrorism court had issued perpetual warrants for Musharraf and he could not evade the Criminal Procedure Code, which demanded his immediate arrest.
The court issued the warrants and declared Musharraf a "proclaimed offender" or fugitive after he refused to cooperate with investigators probing the assassination of former premier Benazir Bhutto.
Prosecutors have accused Musharraf of failing to provide adequate security to Bhutto when she returned to Pakistan from self-exile in 2007.
As a fugitive, Musharraf will not be entitled to any relief unless he surrenders to a court of competent jurisdiction.
Musharraf will be treated in accordance with relevant sections of the Anti-Terrorism Act of 1997 and produced in the anti-terrorism court after his arrest, Ali said.
Musharraf would be able to avoid arrest if he obtains protective or transitory bail from any High Court, Ali said.