Two members of Mejia's security unit were also killed in the operation while police have detained three others.
Mejia and his brother Victor allegedly started off trafficking cocaine before joining with Colombia's far-right paramilitaries.
When the paramilitary warlords surrendered, the two brothers went on the run.
A US court issued extradition warrants against the two in 2004, saying at the time they had shipped nearly 70 tonnes of cocaine in just two years.
Alvaro Uribe, the Colombian president, has called on police to bring down the Mejias' organisation, which is thought to contain dozens of smugglers and hired killers.