Drug traffickers and guerrillas have infiltrated senior levels of the Colombian armed forces, seriously compromising their work, officials say.
Colombia is the source of much of the world's cocaine
Defence Minister Juan Manuel Santos said the Farc rebels and the main drugs cartel had bribed officials to get information and so avoid capture.
His admission confirms the suspicions of many Colombians, correspondents say.
Colombia remains the biggest exporter of cocaine despite billions of dollars in mainly military aid from the US.
Mr Santos told reporters that there were indications the security forces had been infiltrated at a very high level.
"But the important thing is that we have detected this and are doing our utmost to continue the investigation and bring those responsible to justice," Mr Santos said.
Mr Santos's comments come after two incidents pointed to serious leaks in the security forces.
The first was the arrest of a senior defence department official for allegedly passing information to the powerful Norte del Valle drug cartel.
Montoya: US is offering $5m for information leading to his arrest
Its head, Diego Montoya, is on the FBI's "Ten Most Wanted" list, accused of exporting hundreds of tons of cocaine to the US.
The second was earlier this year when sensitive government material was found on guerrillas from the Revolutionary Armed Forces of Colombia (Farc) who had been killed in combat.
The computer files contained classified information going back several years that would be available only to an informant with very high-level access, officials said.
Mr Santos said counter-intelligence operations were being reviewed. He insisted that national security had never been put at risk and said that more arrests were expected.
But the BBC's Jeremy McDermott in Colombia says the minister's admission helps to explain why Diego Montoya has been able to avoid capture despite $5m (£2.5m) offered for information leading to his arrest.