Police made the discovery after a suspect they were following bolted into the mosque, apparently seeking safe haven. Two suspects were killed during a shootout, after which police discovered dozens of hostages.
Ugandan police stumbled onto a "radicalization center" at a mosque in the capital, shooting dead two suspects, arresting dozens more and freeing more than 100 women and children being held against their will, officials announced Saturday.
The confrontation occurred Friday as police were pursuing a suspect thought to have been involved in a high-profile kidnapping and murder earlier in the year. Police followed the man into the Usafi Mosque in Kampala and discovered it was a den for militants.
Two of the alleged militants were shot dead during the ensuing shootout, and one police officer was wounded.
Subsequently, 36 suspects were arrested and charged with hoarding weapons. Police also discovered 18 women and 94 children being held against their will inside the mosque.
"A number of children and women, suspected to either have been kidnapped or held hostage, were rescued," police spokesman Emilian Kayima told a press conference on Saturday.
"Two of the hostage-takers were shot dead after violently attacking and severely injuring one of the security officers," Kayima added.
He said the original suspect whom the police followed into the mosque was taken into custody.
Police are continuing to investigate the connection between the original suspect and the militants found inside the mosque.
The men taken into custody are suspected of being involved with the kidnapping and illegal detention of the women and children. Some of the detainees were Ugandan but others came from neighboring East African countries, including Kenya, Rwanda and Burundi.
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Police also confiscated 23 machetes, dozens of bullets and a bow and arrow after the shootout.
Police believe that the suspect they were following realized he was being trailed and ran into the mosque to seek safe haven.
Interior Minister Jeje Odong said police were taken by surprise when they discovered the weapons, women and children inside the mosque, it was not "planned or intended," he said.
"If the suspect had not gone into the mosque we would have had no reason to enter," Odong said. "We take strong exception to places of worship being used to commit crime."
The children discovered inside the mosque "looked scared and traumatized," Odong added.
Earlier this year, after a member of a prominent Ugandan family was kidnapped, a series of ransom demands were made. But in February, three weeks after her abduction, the body of Susan Magara was found.
The crime shocked Ugandans, and President Yoweri Museveni ordered intelligence agencies to lead an investigation into her murder.