The court has already declared the former military ruler an "absconder" in the Bhutto assassination case as he has not agreed to clarify his position in court despite several notices.
The Federal Investigation Agency (FIA) had requested the court to summon Musharraf, who was President at the time of the assassination, and has refused a request to cooperate in the investigation into Bhutto's death.
Following the lack of cooperation by Musharraf, he was named an "absconding accused", FIA prosecutor Chaudhry Zulfiqar said.
The FIA today presented a final report in the court about Musharraf's refusal to appear and the court issued orders to confiscate his property.
Local media reported that the court has also ordered freezing of Musharraf’s bank’s accounts.
The court ruled that the trial of Musharraf will be started separately from other accused and after he is arrested.
The anti-terrorism court is conducting the trial of five terror suspects, including alleged members of the Tehrik-e- Taliban Pakistan, who have been charged with planning and facilitating the assassination.
Bhutto was killed by a suicide bomber shortly after she addressed an election rally in Rawalpindi on December 27, 2007.
The chargesheet said that former Rawalpindi Police chief Saud Aziz and former Superintendent of Police Khurram Shahzad, who were arrested this year by the FIA on charges of negligence in providing security to Bhutto, were acting on the orders of Musharraf.
Both former police officers were bailed out but are still being tried in the case. The FIA's charge against Musharraf is one of a long list of legal and criminal cases against the former military ruler, who resigned in August 2008, and it could cause problems for his planned return to Pakistani politics.
Musharraf, who has been living in self-exile in Britain since April 2009, has said that he intends to return to Pakistan before the next general election in 2013.
He has also formed a new party, the All Pakistan Muslim League, with an eye to the next election.
A UN Commission, which probed Bhutto's assassination, had held Musharraf responsible for failing to provide adequate security to the former premier after her return to Pakistan from self-exile in October 2007.