The men were reportedly dragged from the police station where they were being held in the remote northeast.
Apur Bitin, an officer in the Arunachal Pradesh town of Tezu, said more than 15 members of the force were injured by the angry group, which heavily outnumbered police.
Prior to the lynching, local media had named the suspected perpetrators and relayed details of the crime.
They reported that the girl’s decapitated body had been found in a tea garden nearly a week after she went missing on 12 February.
Following the arrests of the suspects, the group reportedly demanded the men be handed over by police before dragging them from the police lock-up and attacking them on Monday.
The incident awakened memories of violence in the bordering state of Nagaland, where in 2015 a man suspected of rape was stripped naked, dragged through the streets and beaten, before being hanged by a mob.
Some at the time blamed xenophobia for the flare-up of vigilante violence and 42 people were charged in connection with the lynching.
In the northern state of Himachal Pradesh, the rape and murder of a teenage girl was followed by a suspect being killed in custody in 2017, while in nearby Haryana, the gang rape of two schoolgirls created shockwaves last month.
Arunachal Pradesh’s top elected official, Pema Khandu, has ordered a magistrate to investigate.