Colombia's Supreme Court on Wednesday ordered the "immediate release" of a former rebel leader accused of drug trafficking and shot down revisions to the country's peace accord in a double blow for President Ivan Duque.

Jesus Santrich is suspected of participating in the trafficking of 10 tons of cocaine to the US, which is seeking his extradition, and has been in prison since April 2018.

Santrich was on a list of members of the newly created Common Alternative Revolutionary Force political party due to taking up one of 10 congress seats reserved for the communists as part of the historic 2016 peace accord that ended more than a half century of armed conflict.

The pact stipulated that the Revolutionary Armed Forces of Colombia (FARC) would turn into a political party, with 10 seats reserved in congress until 2026. But Santrich, who is blind, was captured by authorities before he could take up his senate seat.

Although the 52-year-old was released from detention earlier this month, following an order by the special peace court tasked with judging crimes committed during Colombia's long armed conflict, he was re-arrested as he left prison.

The Supreme Court said it - and not the lower courts - were responsible for handling the case of Santrich, whose real name is Seuxis Paucias Hernandez, due to his status as an elected lawmaker.