He is expected to be extradited to the US.
Brazilian police said Ramirez Abadia is suspected of ordering the murders of hundreds of people in Colombia and the US, including police and informers.
He is said to have had plastic surgery to alter his appearance.
In a March 2004 indictment issued by a federal grand jury in Washington, Ramirez Abadia is accused of shipping about 500 tonnes of cocaine worth in excess of $10bn from Colombia to the US between 1990 and 2004.
The gang invested the money in real estate, including mansions and hotels, industry and cars. The operation was carried out across six states.
Ramirez Abadia has been involved in drug trafficking since at least 1986, the US state department said. He was previously indicted in the US in 1994 and 1996 but the Colombian government turned down extradition requests.
He has served prison time in Colombia, but carried on his activities from behind bars.