Police officers in Ciudad Juarez in northern Mexico detained their commander at gunpoint, accusing him of corruption and links to drug gangs.
More than 200 federal police agents raided the hotel where their commander was staying and accused him of planting drugs on police officers to blackmail them into carrying out extortion.
The commander has been suspended, pending an investigation.
Ciudad Juarez is the most violent city in Mexico and corruption is rife.
While some agents blocked off nearby streets to prevent their commander from escaping, others moved into the hotel where he was staying.
They raided his room, where they say they found weapons and drugs.
The federal officers allege that they were part of a stash, which their commander would plant on officers who refused to take part in his corrupt dealings.
They say he would then blackmail the agents into carrying out extortion and other crimes.
The police officers held their commander captive until the Federal Police Commissioner General agreed to suspend him, pending an investigation.
One of the policemen who took part in the protest told the Associated Press news agency corruption in the higher ranks was putting them in danger.
"We risk our lives, we leave families behind and it's the fault of those officers that we go down," he said.
"We are just used as cannon fodder when we could be stopping crime in Juarez," he added.
About 5,000 federal police officers were deployed to Ciudad Juarez in April.
They replaced the army, which had failed to stop a wave of drug-related killings, which has left an estimated 1,700 dead in Ciudad Juarez this year.
The border city is at the centre of a violent battle between rival drug cartels for control of lucrative drug routes to the United States.