Sister Marguerite Bartz, 64, failed to show up at Sunday Mass and a colleague who went to check on her discovered her body. Investigators believe Bartz was killed sometime between Saturday night and Sunday morning, but FBI Special Agent Darrin Jones said he could not disclose any details about how she died.
The FBI and state police were searching her residence for any clues.
Authorities and officials with the Diocese of Gallup, which oversees the parish in Navajo, said they were not sure whether Bartz or the church were the target, or if the attack was a random act.
Authorities were also searching for Bartz's vehicle, a beige 2005 Honda CR-V with a New Jersey license plate, and asking anyone who spoke to Bartz on Saturday night to contact investigators.
Bartz was one of more than a dozen Sisters of the Blessed Sacrament who are currently ministering within the Diocese of Gallup, which spans 55,000 square miles in New Mexico and Arizona.
The diocese said Bartz was born in Plymouth, Wisconsin, in 1945. She entered the order in 1966 from Beaumont, Texas, and professed final vows in 1974. She had ministered in Massachusetts, Louisiana and in several communities around New Mexico before ending up at St. Berard in 1999.
The diocese said there is usually another sister who lives at the residence with Bartz, but she was out of the state at a meeting and Bartz was alone.
"She was known to be a woman always passionate for justice and peace, and the life she lived would tell us that she would respond to this incident with a spirit of forgiveness towards whoever is responsible for these acts," the diocese said in a statement released Monday.