Police secured the area near Belleville, Ontario, Canadian National Railway Co (CN) said, and one train was allowed to pass in the evening.
Soon after, however, protesters set a large fire on the tracks and firefighters were called to put it out, raising doubts as to whether the line will remain clear.
"CN is pleased that the illegal blockade in Tyendinaga has come to an end," the company said in an earlier statement, without saying when rail services would resume.
Tyendinaga Mohawk campaigners barricaded the line in solidarity with the Wet'suwet'en from British Columbia, who are seeking to stop construction of a gas pipeline over their land.
Dozens of Ontario Provincial Police (OPP) descended on the site of the blockade a little after 8 a.m. ET.
Media were kept at a distance. But a group called Real People's Media, which is affiliated with an indigenous clan, posted a video on Twitter showing police wrestle two men to the ground after they refused to back away from the tracks.
"All demonstrators were given the option of leaving the site or being arrested. Ten people were arrested and face multiple charges. All have been released on conditions," the OPP said in a statement posted on Twitter.
CN obtained an injunction on Feb. 7 against those preventing rail traffic from running along its trunk line near Belleville, but provincial police took their time to enforce it in a bid to ease tensions.
In Ottawa, hundreds of protesters met in front of parliament and marched through downtown in support of the Wet'suwet'en.
"We worked extremely hard to obtain a peaceful solution to this situation, but we couldn't allow these barricades to continue," Prime Minister Justin Trudeau said in parliament.
On Friday, Trudeau demanded aboriginal groups lift the rail blockades amid railroad layoffs and shortages of goods like propane.
Trudeau has said it is his government's priority to reconcile with indigenous peoples, who face higher levels of poverty and violence and shorter life expectancies than the national average.
Indigenous Services Minister Marc Miller said the government was still seeking dialogue with the Wet'suwet'en and is "even more committed to a peaceful solution".
The Wet'suwet'en band in British Columbia has been fighting the construction of TC Energy Corp's planned Coastal GasLink pipeline for a decade. Savvy social media use and years of outreach have won the group allies from across Canada.
(Reporting by Chris Helgren in Tyendinaga, Ontario, additional reporting by David Ljunggren in Ottawa and Allison Lampert in Montreal, writing by Steve Scherer; Editing by Chizu Nomiyama, David Gregorio and Richard Pullin)
By Chris Helgren
