"Three of our soldiers have been killed by a mob and investigations are going on to establish the circumstances under which the soldiers were killed," the official Peter Debele told AFP.
"Three guns have been recovered from the scene of the attack and eight people have been arrested in connection with the killing of the soldiers," he added.
Debele said the armed soldiers were attached to an army unit guarding the Ugandan border point of Vurra.
The government earlier this year banned civilians from donning any type of camouflage due to the number of criminals donning military-style gear.
The soldiers, some eight kilometres (five miles) from their post, were stopped by residents for "questioning, they handed over the guns but the mob turned rowdy and lynched them alleging they had come to rob them," said Debele.
Ugandan police spokeswoman for the region, Josephine Angucia told AFP that among the dead soldiers was a unit commander attached to the customs border post, Corporal Julius Kobum.
"We urge the public not to take law into their hands whenever they are faced with any challenge. They should have reported to police," she added.
Uganda's border region experiences high levels of crime due to porous borders used by armed groups to rob and attack local populations.
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