Police official Shyam Lal Gyawali said authorities were investigating the two blasts, which occurred about an hour apart in two Kathmandu neighborhoods.
Police said they suspect that a group that once split from the ruling Communist party was responsible for the explosions because its members have been protesting the arrests of their supporters by the authorities.
The first explosion occurred in northern Kathmandu, killing two people and injuring four, police said. The second blast was in a house in the central part of the city, killing one and injuring one.
Police believe the men in the house are linked to the outlawed group, which is known for violence. They said they found pamphlets from the group at the second explosion site.
The areas around the two blast sites were quickly closed by police and the injured were taken to hospitals.
Security forces were put on high alert and officers were patrolling key areas of Kathmandu.
The splinter communist group split from the Maoist party, which fought government troops from 1996 to 2006, when its members gave up their armed revolt to join a peace process and mainstream politics.