Striking teachers and leftist activists occupied much of the colonial city four months ago, storming Congress and blocking hundreds of streets in an effort to oust state Governor Ulises Ruiz.
Fears of violence before Mexican President-elect Felipe Calderon takes office in December had eased after protesters tentatively agreed this week to loosen their grip while a Senate commission studies whether Ruiz has lost control.
But gunmen shot at a group of about 100 masked protesters who roamed Oaxaca in hijacked public buses, demanding government workers who were trickling back to their offices go home.
A Reuters photographer saw a gunman firing a pistol at masked, fleeing protesters as a handful of people ran out of one government building. Protest leaders said one demonstrator was wounded by the gunfire.
News reports said teachers had postponed a planned return to classes pending a decision on Ruiz's future, and that a group of senators who planned to visit the city on a fact-finding mission today had called off the trip.
A protester displayed several bullet casings he had picked up in the street.
"Every time we get near a solution ... there are violent people who act in this way," said Interior Minister Carlos Abascal.
The protesters accuse Ruiz of stealing an election, using police violence to break up demonstrations and ignoring widespread poverty in Oaxaca.