Benazir Bhutto, the two times Prime Minister of Pakistan, was killed in firing and suicide attack in the garrison city of Rawalpindi in Dec. 2007 when Musharraf was ruling the country.
The Musharraf government had blamed the then Taliban leader Baitullah Mehsood for Benazir's killing, a charge denied by Pakistani Taliban.
No group has so far claimed responsibility for the killing of Benazir Bhutto.
The investigators Monday presented a report in the court in Rawalpindi, listing Musharraf as one of the accused in the case. The documents said that Pervez Musharraf had been issuing instructions to then two senior police officers, responsible for the security of Benazir Bhutto.
Federal Investigation Agency (FIA) prosecutor Chaudhry Zulfiqar told the court that Musharraf had been named as an "absconding accused" as he has shown lack of cooperation.
A United Nation inquiry report said last year that the attack on Benazir Bhutto could be averted if tight security measures had been taken.
The anti-terrorism court is conducting the trial of five suspects, including members of the banned Tehrik-e-Taliban Pakistan, who have been charged with planning and facilitating the assassination. All have denied any involvement.
A prosecutor for the FIA told the court that Musharraf had been called several times in connection with the investigation but he did not appear and he has been declared absconder.
The prosecutor requested the court to declare Musharraf as absconder until the next hearing on Feb. 12, and if he failed to appear at the court, he should be declared proclaimed offender.
The investigators also produced forensic report of Benazir Bhutto's BlackBerry phone, she had used on the day of her murder.
A spokesman for Musharraf dismissed the FIA report as a politically motivated move and said it is aimed at hiding the real causes of the murder of Benazir Bhutto.
Musharraf, who has been living in self-exile in Britain since April 2009, has said that he intended to return to Pakistan before the next general election in 2013. He formed a new party, the All Pakistan Muslim League, with an eye to the next polls.