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.
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 that 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.
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