The third person had sought refuge inside the church in the village of Cerocahui before all three were killed around 6 pm local time (8 pm ET), according to a statement from the Chihuahua state government.
In a statement, the Society of Jesus, the religious order also known as the Jesuits, condemned the killings of the two priests.
It also asked Mexican authorities to recover their bodies, which it said had been removed from the church “by armed individuals,” according to the statement.
In a separate statement, the organization identified the priests as Javier Campos Morales, 79, and Joaquín César Mora Salazar, 80.
The Society also asked for increased protection for residents of Cerocahui and the wider Sierra Tarahumara region.
Violent attacks are a problem in the region, which the Society described as under-policed.
Following the killings, Mexico’s National Guard and the Ministry of Defense mounted an operation to secure the area, according to authorities.
During his morning press conference on Tuesday, Mexican President Andrés Manuel López Obrador also said authorities were “looking into the situation.”
“It’s an area with a strong presence of organized crime,” he said. “It appears that there is already some information on those who were possibly responsible for these crimes.”