The bodies of 22 women, 15 men, 10 girls and eight boys wrapped in black polyethene bags were loaded onto a trailer to be taken to the municipal cemetery for burial later, said Assuman Mugenyi, a police spokesman.
Mugenyi said the bodies were found in three graves inside the garage. He said they bore no external signs of violence and the cause of death would have to be determined by pathologists.
Dozens of police and soldiers kept reporters and photographers 150 yards away from the property in Ggaba, outside Kampala, as the bodies were being dug up. Mugenyi said the digging had stopped and authorities did not expect to find more bodies.
The grisly discovery came a month after authorities dug up 394 bodies from under the floorboards and in the yards of houses owned or rented by leaders of the Movement for the Restoration of the Ten Commandments.
The deaths of what authorities said were 530 people in a March 17 fire in the cult's compound in Kanungu in southwestern Uganda were first believed to be a mass suicide. But after the other bodies were discovered, authorities began to speak of mass murder.
The house in Ggaba had been rented by Dominic Kataribabo, an excommunicated Roman Catholic priest in whose compound in the southwestern village of Rugazi 155 bodies were exhumed on March 28 and 29.
Kataribabo obtained a masters degree in religious education from Loyola Marymount University in Los Angeles in 1987 and worked for several years as a parish priest in the area.
Neighbors said Thursday that four women and two boys had been living in the small, brick house until March 14, three days before the fire in Kanungu.
They said Kataribabo had been a regular visitor at the house and busloads of people would go to the house to pray.
Police have issued warrants for the arrest of cult leaders Kataribabo, Joseph Kibwetere, Credonia Mwerinde and three others. They were initially thought to have perished in the Kanungu fire.
Earlier Thursday, Interior Minister Edward Rugumayo was grilled by legislators on the conditions under which 50 unprotected, barefoot prisoners had dug up the other bodies in several villages in southwestern Uganda.
He said because of the difficult conditions under which they worked, some of the prisoners were suffering from post traumatic stress syndrome.
He said he had been misquoted earlier as saying the prisoners had gone mad.
After the discovery of the 394 bodies, many of which bore signs of stabbing and strangulation, further exhumations were stopped following complaints from opposition politicians and the public after seeing images of the prisoners stripped to the waist handling the decomposing corpses.
Police later said efforts to exhume more bodies from other suspected graves had been put off until proper equipment, including gloves, had been received.