Survivors of the attack, which occurred Tuesday, claimed nine people had been killed, army spokesman Major Shaban Bantariza said.
"The helicopter was pursuing a rebel group that had been seen in the area on Tuesday, but unfortunately at the same time some people had gathered to bury a colleague who had been killed by the rebels," Bantariza said.
"When the mourners saw the helicopters, they ran away and hid themselves in some huts, prompting the helicopter to mistake them for rebels and open fire, killing several of them," he said.
"The incident was regrettable," the army spokesman added.
Bantariza said an investigative team had been dispatched to the area to confirm the death toll.
Reports from Gulu town indicated that more people might have been killed in the incident, which took place near the Moroto river bordering the northeast Ugandan district of Katakwi and the northern Lira district.
Rebels from the Lord's Resistance Army (LRA) have been fighting government forces in northern Uganda since 1988, purportedly to replace President Yoweri Museveni's secular regime with one based on the biblical Ten Commandments.
The rebel group recently left its traditional area of operation and strayed into northeast Uganda region, where the army has been trying to contain its movements.
The LRA's campaign has been marked by the brutal killing and maiming of thousands of civilians, with more than 800,000 people displaced from their homes into squalid camps dotting the entire northern region.