Survivors said the attackers set fire to huts and threw about 70 children into the flames.
The army says the attacks took place two weeks ago but news of them has only now reached the capital, Kampala.
The massacre was discovered by chance, when troops were investigating another attack by suspected Karamojong warriors in the area, regional army commander Lieutenant-Colonel Geoffrey Kakama told the New Vision newspaper.
He said the raiders attacked the villages of Turutuko and Wolinyang in north-east Uganda on 29 July with the help of about 500 Turkana raiders from north-west Kenya.
Lt-Col Kakama said village chiefs had not informed the authorities, for fear of reprisals.
Guns replace spears
Although cattle rustling has long taken place in the area, in recent years the raiders have started using guns as well as spears.
Many of the tribespeople in the area are nomads, herding goats and cattle.
Last month another group of Karamojong warriors ambushed a Ugandan army unit, killing 14 soldiers and injuring 12 others.
Four attackers and two members of the local vigilante group were reported killed in the battle.
Kenyan police also said that more than 70 people were killed in July, in fighting between Ugandan and Kenyan tribesmen involved in cattle rustling near the border.
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