Scores of police in body armour swept into the farming town of San Salvador Atenco, 24km north of Mexico City, and hauled off protesters armed with sticks, machetes and petrol bombs on Thursday.
Trouble had started on Wednesday when police tried to evict unlicensed flower traders from a market. A 14-year-old boy was killed in the riots.
Eleven police officers held hostage by protesters were all released, Televisa television station said, and police took control of the town.
A senior security official said at a news conference in the town hall, which had been occupied by the rioters, that "the only objective was to restore the rule of law".
It was the first time that state and federal police had entered the town since protesters blocked a plan by Vicente Fox, the president, to build an airport there five years ago. That stand-off lasted several days.
San Salvador Atenco expelled its mayor and has been under a form of self-rule since then, with local leaders trying to spread the system to neighbouring villages.
The airport defeat and the subsequent failure to bring the area totally under government control have been held up by rival politicians as an example of Fox's supposed weakness in dealing with conflicts.
Fox's rivals say he is weak in
dealing with conflicts (file pic)
Ruben Aguilar, a presidential spokesman, said the violence in Atenco was the work of a small group of people. "I can categorically assure you there is no lack of control here," he said.
The Zapatistas staged a brief but bloody uprising in the Indian-dominated southern state of Chiapas in 1994.
The rebel movement is named after Emiliano Zapata who founded the Liberation Army of the South and fought for fair redistribution of agriculture lands in the Mexican revolution in 1910.
Its leader - who now refers to himself as Delegate Zero but formerly went under the name Subcomandante Marcos - is touring the region at the moment. He has hardened his political stance in recent days, calling for the government to be overthrown and pledging to expel foreign capital.
Zapatista Army of National Liberation, offical site: http://www.ezln.org.mx/
More information about the Zapatista movement and links to other sources can be found at its Wikipedia entry: http://en.wikipedia.org/wiki/Zapatista_Army_of_National_Liberation