The protests were staged following arrests of several leaders of a teachers' group a week ago.
The leaders were arrested allegedly for using union funds for their own benefit, reports said.
The secretary of public security in Oaxaca, Jorge Alberto Ruiz, was quoted in the media as saying that 21 arrests were made so far.
Ruiz confirmed the figures of the deceased and said that 55 and 53 police officials and civillians were hurt in the clashes respectively.
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