The protest took place at Anuradhapura, capital city of North Central Province.
The crew was taking the north-bound train from here heading to Vavuniya and were believed to be travelling to the former LTTE territory of Kilinochchi.
Channel 4 has come under fire over its a series of documentaries which highlighted alleged human rights abuses by Lankan military during final stages of conflict with the LTTE.
They blocked the train from proceeding for nearly two hours.
Also Read
Finally, the police arrived on the scene and convinced the crew to abandon the northern trip and return to Colombo.
The Channel 4 team faced a protest at the international airport here on Monday when they arrived ahead of this week's Commonwealth summit.
Some of the Sinhala majority nationalist groups have called for their expulsion from the country.
Presidential officials said Sri Lankan President Mahinda Rajapaksa yesterday invited the Channel 4 crew to have tea with him when its producer Jonathan Miller encountered him with questions as he was leaving the Commonwealth Business Forum.