Parents of children rescued from Usafi Mosque during a raid by security agencies have been denied access to them.
On Thursday, about 12 parents camped at CID headquarters in Kibuli, Kampala with hope of seeing their children. However, they were told to leave because police are still conducting investigations.
Ugandan police said Saturday they had stumbled upon a "radicalisation centre" at a Kampala mosque, shooting dead two people, arresting dozens and rescuing over 100 women and children.
The children have since been put into police custody as they record statements and the Ministry of Gender and Social development forges a way forward for rehabilitating the victims who are believed to have been radicalised.
Ismail Nsubuga, one of the parents whose three children were taken during the raid, says that the children were not at the mosque, but staying with relatives in a rented house opposite the mosque.
However, the police spokesperson in charge of CID Vincent Ssekate says, police will hand over the children to the parents after investigations have been completed.
During an ensuing shoot-out, police said one officer was wounded, two men were shot dead and 36 arrested and accused of hoarding weapons.
Also inside the mosque were 18 women and 94 children that police said were being held against their will.
Investigations into the connection between the original suspect and those found inside the mosque are continuing.
At the scene, in a particularly poor part of the city, bullet holes pocked the collection of corrugated tin lean-tos and tarpaulin sheets that constitute the mosque, situated in a low-lying area between a bus station and a shipping container park.
In February, the body of Susan Magara, a member of an influential Ugandan family, was found three weeks after her abduction and a string of ransom demands.
The crime shocked Ugandans and President Museveni ordered intelligence agencies to lead an investigation.
Security forces believe that a key suspect who they had under surveillance realised he was being followed and bolted into the mosque.
Internal affairs minister Jeje Odongo said officers chased the suspect into the mosque and that the subsequent discovery of weapons, women and children was not "planned or intended."
"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."
Mr Odong said the children discovered inside "looked scared and traumatised" and appeared to be from Burundi, Rwanda and Kenya as well as Uganda.