"Obviously, everything went wrong here," fire brigade Chief Joseph Mugisa told reporters at the scene in the northern suburb of Kalerwe.
He said city bureaucrats would be probed over whether they had approved the structure for use.
"I just want to believe it was not permitted," he added. "This is the third church incident we have had under similar circumstances: uncompleted, poorly made, occupied, and also collapsing during or after a heavy downpour."
Four people were killed in 2002 when a church collapsed in Makindye, another suburb of the capital. A year later, two people died when another Kampala church collapsed.
"Certainly such a thing should not be permitted to continue," Mugisa said. "Construction cannot take place within the city without the permission of the city authorities, and the city authority is everywhere."No less than 200 born-again Christians were attending a busy prayer service at the City of the Lord church in a suburb of the capital Kampala on Wednesday when torrential rain struck at about 7 p.m. (4 p.m. British time).
Nearly 100 people were badly hurt and rushed to hospitals. The death toll was expected to rise.
Rescuers said the number inside the unfinished building had been swollen by people seeking shelter from the downpour.
There was no immediate comment from city authorities.
Neighbour Wilson Muhoozi, who helped worshippers escape from the rubble, said the building collapsed in two sections.
"People were passing through the windows of the church, so we had to pick them (up). My house was full," he said. "While we were calling police, the other side of the church fell down."
At least two-thirds of Uganda's 27 million people are Christians. A growing number attend evangelical churches that have sprung up across the east African country.
