A covert CIA programme has helped Colombia's government kill at least two dozen leaders of the Revolutionary Armed Forces of Colombia, the rebel insurgency also known as Farc, The Washington Post reported.
The National Security Agency has also provided "substantial eavesdropping help" to the Colombian government, according to The Post.
And the US provided Colombia with GPS equipment that can be used to transform regular munitions into "smart bombs" that can accurately home in on specific targets, even if they are located in dense jungles.
In March 2008, Colombian forces killed a top Farc commander, Raul Reyes, in one of several jungle camps the rebels operated in Ecuador, just across the border.
The Post report on Saturday said Colombia used US-made smart bombs in the operation.
The report was based on interviews with more than 30 former and current US and Colombian officials.
The CIA would not comment on the report. Without going into detail, Colombian President Juan Manuel Santos told The Post that the CIA had been "of help", providing Colombian forces with "better training and knowledge".
The multibillion-US-dollar programme was funded secretly and separately from US$9 billion in aid that the US has openly provided to Colombia, mostly in military assistance.
It was authorised by President George W Bush and has continued under President Barack Obama, the newspaper reported.
Colombia's government and Farc have been engaged in peace talks in Havana since late 2012, but there has been no ceasefire between the two sides.
Earlier this month Santos blamed the rebels for an attack on a police post that killed nine people, including civilians, military and a police officer.
The Farc rebels took up arms in 1964. The US-backed military build-up has reduced Farc's ranks to about 9,000 fighters and killed several top commanders.
The covert action programme in Colombia is one of a handful of intelligence initiatives that has escaped public notice since the September 11, 2001, attacks.