Two large truckloads of protesters were taken away after riot police violently broke up the rally in the central town of Letpadan, according to an AFP reporter on the scene, ending over a week of stalemate between the authorities and students calling for education reforms.
Government spokesman Ye Htut defended the police after Tuesday's violence, saying they were forced to react to provocation by the protesters.
"After many warnings that were not followed, police had to use force to disperse the protest because (protesters) attacked them and tried to destroy barricades," he said in a post on his Facebook page.
The crackdown has intensified concerns that authorities are resorting to the repressive tactics of the previous authoritarian regime, as the nation stumbles towards a general election scheduled for the end of this year that many see as the measure of its democratic progress.
More From This Section
It also comes just days after authorities used violence to end a supporting rally in the commercial hub of Yangon, prompting condemnation from rights campaigners.
Criticising the use of "excessive force" in Letpadan, Phil Robertson of Human Rights Watch said the "disguise has come off and we are back to the bad old Burma of yesteryear," referring to the country by its previous name.
The United States embassy in Yangon also took to Twitter urging "patience, compromise and restraint" on Myanmar's path to democracy.