Musharraf, summoned to face charges of criminal conspiracy and failure to provide security to the former premier, was not brought to the court in Rawalpindi because of threats to his life.
Police and Musharraf's counsel told Judge Chaudhry Habibur Rehman that it was not safe to bring the former military ruler to court due to the threats.
Rehman adjourned the indictment till August 20 and ordered police to ensure Musharraf's presence at the next hearing.
Bhutto was assassinated soon after an election rally in Rawalpindi in December 2007.
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Musharraf, who was then the President, blamed her killing on Pakistani Taliban chief Baitullah Mehsud, who denied any involvement. Mehsud was killed in a US drone strike in 2009.
The former military ruler has been held at his farmhouse on the outskirts of Islamabad since his arrest in April because of threats from the Taliban.
He returned to Pakistan in March after living in self-exile for about five years to contest the general election in May. However, he was barred by a Pakistani court from contesting polls for the rest of his life.