Luis Cardenas Palomino, one of the most senior Mexican federal police officials, has rejected charges of corruption as he announced that he will resign on December 31.
"After 23 years of public service, I have made the decision to move into the private sector," Cardenas, the top cop in charge of regional security, wrote in an open letter posted on Facebook on Saturday.
Cardenas Palomino faces no charges of wrongdoing, but under his watch there was a shoot-out in June between police in the Mexico City airport that killed three officers, and an attack by federal police in August on a US diplomatic vehicle that wounded two US agents.
"As a public official, I have been exposed to criticism, much of it empty and unfounded," including charges of corruption, he said.
"I leave this institution with my head held high, without having committed any act of which I must repent," Cardenas Palomino wrote.
The federal police is being reorganised as part of a major security overhaul by Mexico's new president, Enrique Pena Nieto.
Mexico's congress passed a law last week that closed the ministry of Public Security, a pillar in the fight against drugs under former president Felipe Calderon.
The federal police will now be under the control of the ministry of interior.
Pena Nieto, who took office December 1, runs Latin America's second biggest economy that is also engaged in a relentless drug war that has killed more than 60,000 people in the last six years.
In June federal police smuggling drugs from Peru killed three agents who attempted to arrest them at the Mexico City international airport. Cardenas Palomino eventually replaced all 348 officers responsible for airport security.
In August, federal police opened fire on on what turned out to be a car with diplomatic plates. The attorney general's office has charged 14 federal police officers with attempted murder, while five police commanders have been
accused of lying in the case.