"The three men were probably lynched and then set on fire along with their motorcycles. The identities of the three people were yet to be ascertained," Tinsukia district magistrate Absar Hazarika said by telephone.
One person was killed and about 12 injured on Sunday in the clashes between the two civilian groups.
Authorities on Sunday night clamped an indefinite curfew in Tinsukia district after clashes broke out between tea plantation workers armed with bows and arrows and ethnic Assamese protestors who had blocked a highway in the area for the past week. The blockade was to protest the May 6 killing of 24-year-old Buddheswar Moran, allegedly in a staged shootout by army soldiers.
"The highway blockade agitation had led to shortage of essentials and medicines in and around Tinsukia district and that probably led angry tea garden workers to come out and challenge the protestors," Hazarika said.
Anti-riot police were deployed to bring the situation under control.
Army authorities last week admitted it was an "unfortunate incident" and ordered a probe into the killing of Moran. The Assam government too ordered an independent investigation into the incident.
Assam is home to at least half-a-dozen rebel groups, prominent among them being the outlawed United Liberation Front of Asom (ULFA) that is fighting for an independent Assamese homeland since 1979.
The army is conducting a massive military offensive since January in Assam after the ULFA killed about 80 people and staged a string of bomb attacks in public places.
Over 10,000 people have lost their lives to insurgency in Assam during the past two decades.