The newly elected mayor of Chilpancingo, Mexico, had appointed Germán Reyes as the man who would safeguard his city.

But on Tuesday, the Mexican authorities arrested Mr. Reyes, a retired military officer and former prosecutor, accusing him of ordering the mayor’s brutal killing in southwest Mexico last month in a case that had already shocked a nation reeling from widespread violence against local politicians.

The mayor, Alejandro Arcos Catalán, 43, took office in Chilpancingo, the capital of Guerrero state in southwest Mexico, but disappeared less than a week later. On Oct. 6, his head was found on top of a white pickup, local officials said. The rest of his body was in the front seat of the vehicle.

State prosecutors on Tuesday announced the arrest of Mr. Reyes, 46, the city’s security chief, on a charge of aggravated homicide, saying he colluded with a local criminal group to abduct and assassinate the mayor.

“The fact that the government, at least at the municipal level, may be influenced by a third party to make public security decisions already suggests that the rule of law is at risk,” said José Filiberto Velázquez, a local minister and the director of the Minerva Bello human rights group in Guerrero, one of the poorest and most violent states in Mexico.

During a brief recess in court on Tuesday, Mr. Reyes told reporters that the charge was “absurd.” He said that Mr. Arcos Catalán interviewed him in late September for the job of public security minister and appointed him the next day.