Otoniel, 50 , was captured during operation Osiris in a rural area of Colombia's Uraba region, in Antioquia province.

He is accused of sending dozens of shipments of cocaine to the United States, and Duque says he is also accused of killing police officers, recruiting minors, and sexually abusing children among other crimes.

Colombia had offered a reward of up to three billion pesos (about $A1 million) for information concerning Otoniel's whereabouts, while the US government had put up a reward of $US5 million for help finding him.

"This is the biggest blow against drug trafficking in our country this century," Duque said during a video message broadcast on Saturday.

"This blow is only comparable to the fall of Pablo Escobar in the 1990s."

One police officer died during the operation, Duque said.

Otoniel rose to become the leader of the drug trafficking group the Clan del Golfo, or Gulf Clan, following stints as a left-wing guerrilla and later as a paramilitary.

Clan del Golfo has about 1200 armed men - the majority former members of far-right paramilitary groups - and is present in 10 of Colombia's 32 provinces.

As well as drug trafficking, Clan del Golfo is involved with illegal mining, authorities say.

The government also accuses the group of threatening and killing community leaders across the country.

Though Duque said Otoniel's capture represented the end of the Clan del Golfo, Colombia Risk Analysis director Sergio Guzman said a new leader would surely be waiting to take over.

Colombian authorities launched Operation Agamemnon in 2016 as they worked to close in on Otoniel, killing and capturing dozens of his lieutenants, going after his finances and forcing him to be constantly on the move, according to the police.

Australian Associated Press