The protesters said the proposed project poses a challenge to the livelihood of the people in the delta districts.
Over 280 party activists and farmers were taken into custody at the Thanjavur Railway Station when they picketed the railway tracks.
Rail traffic on the route, including Chozhan Express, was delayed for more than two hours, police said.
At Nagapattinam too, some 300 persons, including farmers who staged a rail roko, were taken into custody, police said, adding, shopkeepers extended support to the protest by downing their shutters.