Aftab Sherpao told reporters "there are at least 47 dead" from the blast that hit a crowd gathered at the city's Nishtar Park on Tuesday to celebrate the birthday of Prophet Muhammad.
Officials at Karachi's Civil Hospital earlier said they had received at least 21 bodies, but television channels reported that another hospital in the southern Pakistani city had received more.
An AFP report claimed that 57 people were killed in the attack.
Television pictures showed dead bodies on the ground and wounded being taken to hospitals in vans after the explosion.
Jehangir Mirza, inspector general of police for Sindh province, told Reuters: "What we know at this point is that there was a blast ... and that there are some injured who are being taken to the hospitals. I cannot tell the number of those injured at the moment."
Some media reports suggested that at least 50 people had been wounded.There were no immediate claims of responsibility, but sectarian violence between Sunni and minority Shia Muslims has plagued Pakistan, and Karachi in particular, for 20 years.
Hundreds of people have been killed in religious violence. In February, at least 40 people were killed when a suicide bomber attacked a Shia procession in the town of Hangu in the country's North West Frontier Province.