Ontario Provincial Police say protesters left the rail lines east of Belleville at around 7 p.m Wednesday. after blocking the tracks for about six hours. No arrests were made.
Passengers traveling between Toronto and either Ottawa or Montreal were delayed by up to two hours Wednesday afternoon.
A spokeswoman for Via Rail said Idle No More protesters were on the tracks near Maryville, between Belleville and Kingston.
At the time, Mylène Bélanger said the rail company did its best to keep passengers on time. She said people were taken to their destinations from Belleville or Kingston by shuttle.
Those who opted not to travel because of the delay will receive a full refund, said Belanger.
Participants in the Idle No More grassroots movement have been staging almost daily protests against the Conservative government's Bill C-45, an omnibus bill which they say violates treaty rights and weakens environment laws.
Protesters blocked Via Rail trains at the same spot on December 30 and January 6.