The packed City of the Lord evangelical church caved in Kalerwe suburb, about four kilometres north of the city centre of Uganada’s capital, Kampala.
The roof fell in during a heavy rain storm as people gathered for a service.
Worshippers suffered crushed limbs and head and chest injuries when the brick and sheet building came down on them.
Emergency workers and police officers scrambled to rescue survivors some of whom were screaming.
"I was here in my house when it was raining, then a heavy storm started. I saw the church building shaking, the storm was moving the roof from one side to the other then it collaped," a witness said.
The survivors were being treated at Mulago National Hospital, about three kilometres north of Kampala.
Junior Health Minister Mike Mukula expressed the government's sympathy for those killed and injured. "We express deep shock over what has taken place today at Kalerwe," he said.
At the hospital at least 100 people hung around outside as they tried to find out the whereabouts of relatives.
Survivors at the hospital said there were more than 1,000 people in the church when the tragedy struck.
The hospital's emergency ward, which normally handles up to 30 cases, was overwhelmed by the injured, with some lying on the floor and others on makeshift beds in the corridor.
Police commander Turyagumanawe said an investigation would be launched into the cause of the accident.
In January 14 people were killed and more than 100 injured in neighbouring Kenya when an unfinished office building under construction collapsed in the capital. The owner of the building faces manslaughter charges.