Police officials said it appeared that six to eight assailants on motorbikes first opened fire on the bus just near the Dow Medical College and then entered the bus when it stopped at Safoora Chorangi, Gulistan-e-Johar area of Karachi.
The attackers killed 47 people, including 16 women, and wounded more than 20 others before fleeing from the scene.
The death toll could further rise as some persons are seriously injured. The injured and dead were shifted to various hospitals by rescue workers.
A senior police official said the attackers entered the bus and shot the passengers in the head.
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A blood-stained pamphlet of terrorist group Islamic State was recovered from the scene, according to a police official. But government has not so far named any group for the attack.
Balochistan-based militant group Jundullah also claimed responsibility for the attack.
A rescue official quoted a victim as saying that the attackers were dressed in police uniforms.
This was the worst attack targeting the members of the minority community after a suicide bomber in January blew himself up in a Shia mosque in Shikarpur in the Sindh province killing 61 worshippers and bystanders.