(CNN) -- Hundreds of Mexican federal police officers from two opposing groups clashed in Ciudad Juarez over the weekend over allegations of corruption within their ranks.

On Saturday, a three-day protest turned into a riot between two opposing groups of the federal police department. The confrontation was triggered by corruption allegations against federal police Cmdr. Salomon Alarcon Romero. Alarcon's critics say the commander has participated in kidnappings, killings and extortion in Juarez, which borders U.S. city El Paso, Texas.

The protest started Thursday after the arrest of an officer who critics say was falsely accused for drug crimes, the state-run news agency Notimex reported.

Local media said about 200 heavily armed officers -- some wearing ski masks -- demonstrated in front of the La Playa hotel, which houses some federal police offices. The group denounced Alarcon and other commanders as corrupt, while calling for a full investigation by the Mexican military into Alarcon's alleged ties with drug traffickers. More than 100 supporters of Alarcon pushed back against the accusers, defending their commanders and deflecting misconduct allegations, local media reported.

Several police officers suffered injuries during the protest, according to Notimex. Alarcon fled in an armored car, the news agency said.

A spokesman for the federal police did not immediately return messages left by CNN. In a phone interview with CNN, Carlos Gonzalez with the Chihuahua state attorney general's office said he had no information about any criminal charges being brought against Alarcon.

Officials from the Ministry of Public Security released a statement Saturday stating four federal police commanders were suspended from the police force and sent to Mexico City to be investigated for misconduct. It was unknown if Alarcon was among those commanders. The results of that inquiry would be available in the coming days, Notimex reported.

Officials at all three levels of government have said that cartels have penetrated the moral structure of police in Juarez and in many other parts of Mexico. Saturday's clash was a telltale sign of the mistrust and skepticism exuding throughout the city. This was the first publicized rift among federal police since they took over control of security in the city from the Mexican military on April 9th.

"It's irresponsible to suggest the cartels have control of this city," Juarez Mayor Jose Reyes Ferriz told CNN in a recent interview. "Their actions indicate signs of desperation. It shows their backs are against the wall."

In 2008, more than 700 municipal police officers left the Juarez force. The majority were fired by Reyes after failing a "confidence test," and others either quit or took early retirement when the test was announced.

In recent weeks, at least two graffiti messages left by drug traffickers alleged ties between the federal police and the Sinaloa cartel. One of the messages asked for the United States to launch an investigation.

The mayor has said in the past that a major contributor to the problems in Juarez has to do with Mexico's judicial system. The country does not practice the death penalty. Also, many suspects who are arrested are never charged, Ferriz said.

"It's just catch and release," Ferriz said.