Bhutto's assassination was one of the most shocking events in Pakistan's turbulent history and remains shrouded in mystery.
"The court has issued warrants and these are non-bailable. They can be arrested anytime," special prosecutor Chaudhry Zulfiqar Ali told Reuters.
"I argued that they were responsible for Bhutto's security and they failed to make foolproof security arrangements and they ordered the crime scene to be hosed down despite resistance from other officials."
Court officials were not immediately available for comment.
Ali named the two police officials as Saud Aziz, former police chief of the city of Rawalpindi, where the attack took place, and one of his deputies, Khurram Shahzad.
Bhutto was killed in a gun and suicide bomb attack after an election rally in the city of Rawalpindi on December 27, 2007, weeks after she returned to Pakistan after years in self-imposed exile.
A report by a United Nations commission of inquiry released in New York in April said any credible investigation should not rule out the possibility that members of Pakistan's military and security establishment were involved.
It heavily criticized Pakistani authorities, saying they had "severely hampered" the investigation.
The Pakistani government may be reluctant to act on a call by a U.N. commission to investigate thoroughly the assassination because of fear of its own powerful security forces, analysts say.
The initial investigation blamed a Pakistani Taliban leader and al Qaeda ally, Baitullah Mehsud, for Bhutto's murder.
Mehsud was killed last year in a missile attack launched by a U.S. drone aircraft.
The U.N. report said no-one believed the 15-year-old suicide bomber who killed Bhutto acted alone, and the failure to examine her death effectively appeared to be deliberate, but the commission did not say who it believed was guilty.
(Editing by Michael Georgy and Daniel Magnowski)