Ugandan police said another 25 bodies had been recovered after weekend fighting in a western kingdom whose tribal monarch is accused of stoking a separatist rebellion, bringing the death toll to 87.
Officials said at least 46 guards and 16 police died when the security forces stormed the palace of Charles Wesley Mumbere, king of the Rwenzururu kingdom, near Uganda's border with Congo.
Mumbere was arrested and has now been charged with murder.
Uganda, however, rejected charges by rights group Amnesty International - who called the killings a "massacre" - that its security forces carried out the extra-judicial killings during the clashes.
"Security forces were being attacked. They had to defend themselves, they had to protect themselves," Jeje Odongo, Uganda's internal minister, told a press conference in the capital, Kampala.
"Security agencies do not have a shoot-to-kill policy. What happened is a situation of self-defence."
Odongo added that weapons, including automatic guns and a cache of crude weapons such as spears and machetes, had been seized following the incident.
At least 149 people were also arrested.
Opposition leader Kizza Besigye also described the killings as a "massacre" and posted a photo on Twitter purporting to show bodies of victims outside Mumbere's palace.
Amnesty International said that many victims seem to have been summarily shot dead.
"The full picture of the weekend's events is yet to emerge, but there appears to be shocking examples of unlawful killings and a complete disregard for human rights during the arrests," Abdullahi Halakhe, Amnesty International's East Africa researcher, said in a statement published on Tuesday.
"In a shocking display of heavy-handedness, many people appear to have been summarily shot dead and their bodies dumped.
"Video footage broadcast by Ugandan TV stations showed bodies of young men apparently dumped on river banks and in bushes, and men writhing in pain as they are tossed off pick-up trucks with their hands tied behind their backs."
The security forces have continued to search for the rebels linked to the tribal king.
Influential tribal rulers
The killings underscore tensions between longtime President Yoweri Museveni and influential tribal rulers who are constitutionally recognised but have no real authority or armies of their own.
Before presidential polls in February, which were won by Museveni, Mumbere came out in support of the opposition, a move that appeared to violate the traditional leaders' code of conduct.
Museveni lost the popular vote in Kasese, and a month later clashes erupted between the security forces and militiamen who were believed to be loyal to Mumbere.
In March, amid clashes between Mumbere's supporters and security officials, Museveni vowed to defeat the separatists, who complain of marginalisation by the central government 340km away in the capital.
Source: News Agencies