The shutdown was called by the Akhil Bharatiya Rashtrawadi Kisan Sanghathan.
Hundreds of activists headed by slain Ranvir Sena chief Brahmeshwar Singh's son Indu Bhusan disrupted road traffic and blocked railway tracks, affecting half a dozen trains.
"Protestors forcibly stopped Jan-Sadharan Express and Patna-Pune Express at Ara railway station for hours," an official said.
Bhojpur Superintendent of Police Rajesh Kumar said: "Sangathan workers forcibly stopped trains at the Ara railway station by squatting on the tracks and disrupted train traffic at other places."
Indu Bhusan heads the Sanghathan, the political wing of the outlawed Ranvir Sena that was founded by Brahmeshwar Singh.
They have demanded a CBI probe into the alleged gang rape of six Mahadalit women, all rag-pickers, who were allegedly gang-raped at gun point in Bhojpur district's Kurmuri village early this month.
One of the three arrested, Neel Nidhi Singh, is a former commander of Ranvir Sena.
However, a district administration official said the shutdown evoked mixed response and only partially hit normal life in Ara, district headquarters of Bhojpur.
He said the Sangathan's members took to the streets to enforce the shutdown in Ara and blocked several roads, crippling the movement of vehicles on Ara-Patna and Ara-Sasaram roads.
Protestors also raised slogans against the state government and burnt effigies of Chief Minister Jitan Ram Manjhi and former Chief Minister Nitish Kumar.