Jesus Santrich, a blind former leader of the FARC rebels, was arrested in April 2018, suspected of participating in the trafficking of 10 tons of cocaine to the United States.
However, the Special Jurisdiction for Peace (JEP) ordered him released to comply with the "non-extradition guarantee" that formed part of the historic 2016 peace accord that brought an end to FARC's 50-year insurrection, converting the former rebels into a political party.
"I hope that the government, the public prosecutor's office and other agencies will respect the decision," Santrich said in an audio recording sent form prison.
Colombia's Attorney General Nestor Humberto Martinez responded to the order by resigning.
The JEP is the special court tasked with judging crimes committed during Colombia's half century of armed conflict.
It had previously suspended an extradition order against Santrich, whose real name is Seuxis Paucias Hernandez.
The 52-year-old is accused of involvement in drug trafficking between June 2017 and April 2018, crucially after the peace accord was signed in December 2016.
The agreement stipulated that former guerrillas who commit crimes after the pact was signed would be tried in a normal court and would lose the benefits afforded by the accord, such as a ban on extradition.
FARC, the Spanish acronym for the Revolutionary Armed Forces of Colombia, which has subsequently become the Common Alternative Revolutionary Force political party, has denounced the accusations against Santrich as a "judicial set-up."
Explaining his resignation, Martinez said: "My conscience and my devotion to the rule of law prevents me" from liberating Santrich.
"That's why I've presented my irrevocable resignation," he added.
Santrich's case had caused a schism between Martinez and the JEP over different interpretations regarding the scope of the special court's jurisdiction.
The JEP said the prosecution's evidence was insufficient to establish both what had taken place and when it occurred. It also said the US had not sent its evidence against Santrich.
It has "adopted a decision that defies the evidence provided by the United States and the prosecutor's office," said Martinez, adding that "the evidence was unequivocal."
Martinez had been under pressure to resign over an unrelated affair, having been implicated in the far-ranging corruption scandal centered around Brazilian corruption giant Odebrecht.
On Tuesday, FARC said one of its former guerrilla leaders, Jorge Enrique Corredor Gonzalez, known as Wilson Saavedra, had been killed by attackers on a motorcycle in western Colombia.
They said he was the second such former guerrilla leader killed since the peace accord was signed.