The reshuffling comes nearly two months after a shooting sent passengers scrambling and left shattered glass on the ground near a food court at the airport.
The two officers accused in the shooting, Daniel Cruz Garcia and Zeferino Morales Franco, remain at large. Authorities are offering a 3.4 million-peso ($260,000) reward for information leading to their capture.
Officials allege that Cruz and Morales opened fire on their fellow officers, who were attempting to arrest them after an investigation showed they had ties to a drug trafficking cell. Cruz and Morales told Proceso magazine last month that they had no connection with drug trafficking and were being targeted because they had threatened to denounce drug ties within airport police ranks.