There were no immediate reports of casualties following the gunfight in Nueva Italia between the self-defense forces and the Knights Templar gang in Michoacan state, the senior state government official said on condition of anonymity.
On its Facebook page, the Tepalcatepec vigilante force said around 100 pick-up trucks entered Nueva Italia and that a "light confrontation took place at the entrance, everything is fine."
The growing civilian militia movement, which first emerged in Michoacan nearly a year ago, has seized more communities in recent weeks in their bid to oust the Templars from the state.
Interior Minister Miguel Osorio Chong has said the self-defense units are illegal. Yet some critics charge the government is protecting them.
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Vigilante leaders have stated that Apatzingan was a key target because it is a Templar bastion and a vital economic hub for their limes, avocados and mangos.
A fire was sparked in the city's municipal office on Friday in an apparent arson attack.
Opponents of the vigilantes have burned trucks and buses in the past week to protest the militias' incursions in the region.
The Templars have accused the vigilantes of being a proxy force for the rival Jalisco New Generation drug cartel, a charge the militias deny.
Michoacan, where more than half the population is living in poverty, has emerged as one of President Enrique Pena Nieto's biggest security nightmares. He inherited a war on organized crime and drug traffickers that has left 77,000 people dead in the past seven years alone.