The court has already declared Pervez Musharraf as an " absconder" in the assassination case of Benazir Bhutto 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 Pervez Musharraf who was President at the time of the assassination, but he had refused a request to cooperate in the investigation into Bhutto's death.
Following the lack of cooperation by Musharraf, he was named as an "absconding accused", FIA prosecutor Chaudhry Zulfiqar said.
The FIA on Saturday presented a final report in the court about Pervez Musharraf's refusal to appear and the court issued orders to confiscate property of the former president. Local media reported that the court has also ordered to freeze Musharraf's bank 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 charge sheet further 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 and are now 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 president 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, said that he planned 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 polls.