Diego Murillo, also known as Don Berna, turned himself in last month after a three-day manhunt.
The US wants him extradited, but a senior minister said any decision would rest with President Alvaro Uribe.
Mr Murillo's role as a negotiator for the far right AUC group grants him effective immunity under Colombia's ongoing peace process.
Colombia's interior and justice minister, Sabas Pretelt, said that all legal proceedings against Mr Murillo would be suspended as long as he remains in peace talks.
Colombia's government is attempting to negotiate a settlement with right-wing paramilitary groups, who are blamed for a string of massacres throughout the country.