The police said the three were killed in Kokrajhar district, taking the toll in recent violence to 64.
More than 170,000 people have fled their homes after fighting between indigenous Bodo tribes and Muslim settlers in Kokrajhar and Chirang.
There has been tension between indigenous groups and Muslim Bengali migrants in Assam for many years.
Senior Assam police official LR Bishnoi told the Press Trust of India news agency that three people were killed in Ranibui village in Kokrajhar late on Monday after some “Bodo miscreants fired indiscriminately”.
A curfew has been imposed in Kokrajhar after the incident.
Police say that the clashes began last month when unidentified men killed four youths in Kokrajhar, an area dominated by the Bodo tribe.
They say that armed Bodos attacked Muslims in retaliation, suspecting they were behind the killings.
Soon afterwards unidentified groups set houses, schools and vehicles ablaze, police said, firing indiscriminately from automatic weapons in populated areas