“The accords are clear: Whoever commits a crime after the signing of the deal will be sent to the courts for the new crimes committed,” Mr. Santos said.
FARC leaders rallied around Mr. Hernández on Monday, contending that the government was breaking the peace deal by ordering the arrest.
“What they’ve done to Jesús Santrich they can do to any of us,” said Judith Simanca Herrera, a former FARC leader known by her war name, Victoria Sandino.
The arrest, which officials said involved information from the Drug Enforcement Administration, also showed the American involvement in continuing to capture FARC leaders when they are wanted on trafficking accusations.
United States officials have warned repeatedly that former guerrillas have not left the drug business and continue to have involvement in the American market.
Néstor Humberto Martínez, the Colombian attorney general, said Mr. Hernández had access to planes registered in the United States to transport drugs, as well as cocaine laboratories. He said Mr. Hernández had been involved in drug smuggling scheme until this month.
Mr. Hernández cut a striking figure among the former rebel leaders, appearing before reporters wearing dark sunglasses and a checkered scarf similar to those worn by Palestinian rebels.
A top commander, he was a key member in negotiating the peace deal signed with Mr. Santos in 2016. In the months since, he had taken a political position in the new rebel party. He had even been selected to take one of the seats in Congress that the party was granted automatically as part of the deal.
Both the peace accord the party remain unpopular in Colombia, and Mr. Hernández’s arrest is likely to stoke longstanding suspicions among Colombians that FARC members have not given up the drug trade.
By Monday evening, it had already become the key topic among candidates in the first round of Colombia’s presidential election.
“Colombian authorities must act firm and investigate what other heads of this organization continue to have criminal ties,” said Ivan Duque, a front-runner in the race, which is set for May. His right-wing party, Democratic Center, campaigned against the peace deal, saying it was too lenient on the rebels for drug crimes.
The arrest also capped what has been a disastrous year for the FARC’s political party.
In February, the group said it was suspending campaigning after many of its members had been attacked by angry mobs on the campaign trail. In March, its former commander, Rodrigo Londoño, dropped out of the presidential campaign, citing health problems.
Several days later, Colombians delivered a deep blow to the group during congressional elections, in which it won less than 1 percent of the vote.