People from several surrounding communities were protesting in the central square of San Juan Chamula when "individuals opened fire," said Juan Carlos Gomez Aranda, secretary general of the Chiapas state government.
The victims included the mayor, Domingo Lopez Gonzalez, town administrator Narciso Lunes Hernandez and councilman Miguel Lopez Gomez. The two others were a municipal government driver and a town resident.
Twelve other people were hurt and taken to hospitals.
The protesters demanded the construction of public works projects and that the town pay an arts program in cash, Gomez Aranda said.
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The government urged the population to "maintain calm and trust that justice will be served."
The Zapatista National Liberation Army (EZLN), a rebel movement that led a brief uprising in Chiapas in 1994, had warned this week that "discontent and division" in San Juan Chamula could trigger "an internal conflict."
Two weeks ago, residents protested in Chiapas' capital, Tuxtla Gutierrez, and blocked a road. Police broke up that protest with tear gas.
San Juan Chamula is a majority indigenous and Catholic town of 87,000 people that has been hit in the past by conflicts with Protestants.