One of Mexico's top federal police officials has announced his resignation, rejecting charges of corruption and promising to elaborate on his motivation after he steps down in January.

The move by Luis Cardenas Palomino, the top cop in charge of regional security, comes as President Enrique Pena Nieto seeks to bring the federal police under the control of the interior ministry as part of a major security overhaul.

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.

"After 23 years of public service, I have made the decision to move into the private sector," Cardenas wrote in an open letter posted on Saturday on Facebook, revealing his intention to resign on December 31.

"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," he added, promising to speak more freely in January after he steps down.

Pena Nieto, who took office December 1, has vowed to increase public safety in the face of a relentless drug war that has killed more than 60,000 people in the last six years.