Nine beheaded bodies were found Sunday, the San Diego Union-Tribune reported. They were accompanied by a sign that read "We worked for El Gordo Villareal," a reference to a leader in the Arellano Felix drug cartel.
The bodies included those of three police officers.
The nine were among at least 38 people killed between Saturday and Monday, the Los Angeles Times said. Other victims included a man and his two sons, 4 and 13, who were shot Saturday night, and the nephew of Baja California's tourism secretary.
Mayor Jorge Ramos replaced the police chief, Alberto Capella Ibarra, with his deputy, a military officer, Lt. Col. Julian Leyzaola.
Capella, a lawyer, was put in charge of Tijuana police after serving as head of a citizen's committee and surviving an assassination attempt.
"The city government recognizes that Alberto Capella is a citizen who gave his best effort for Tijuana as a civilian fighting for public safety, and later as secretary of public safety," a statement from the mayor's office said.