One of those killed in clashes has been identified as Maoist unit commander Sadhuram, said an army source on Wednesday.
The clash occurred on Tuesday night when a group of Maoists attacked a security force patrol team at Babasi in Dolkha district, about 140km northeast of Kathmandu, said the unnamed source.
Arms and ammunition were also seized. The source also said the army had on Monday used helicopters to bomb a large group of Maoists who had gathered to declare a regional autonomous government in the remote Jajarkot region in northwestern Nepal.
Newspapers on Wednesday claimed 40 Maoists had died in the bombing, but rebel sources said only one rebel and several villagers had been killed.
The press reports said top Maoist leader Baburam Bhattrai and other central committee members attended the meeting, which was to announce the Bheri-Karnali Autonomous Government, but had survived the attack.
Villagers claimed they had been forced to attend the gathering at Junga Thapachaur by the rebels, who told them to bring blankets and food for their own consumption.
The rebels threatened to break the hands, legs or necks of those not obeying the order, said villagers.
The rebels are battling to overthrow the monarchy and install a communist republic in the Himalayan nation. Their rebellion has claimed more than 9000 lives since 1996.