Asked about a report on Pakistan's ARY TV network that the militant group founded by Osama bin Laden was to blame for Thursday's assassination, interior ministry spokesman Javed Cheema said the government did not know about that claim.
But he said the likely culprits were "the same extremist elements who have been perpetrating acts of terrorism in the country in the past."
Pakistan has repeatedly said Taliban and Al-Qaeda linked groups are behind the unprecedented wave of attacks this year that has left more than 800 people dead.
President Pervez Musharraf blamed Al-Qaeda when he survived two assassination attempts in 2003 in Rawalpindi, the same town where Bhutto was killed in a gun and suicide attack.
Pakistan said Al-Qaeda number three Abu Farj Al-Libbi was the mastermind of the attacks on Musharraf.
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He was arrested in 2005 and handed over to the United States.
Islamist militants have been waging an increasingly aggressive campaign in Pakistan.
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