The hard-won deal to end Colombia’s decades-long civil war was thrown into doubt on Thursday after the top peace negotiator for the leading rebel force, known as the FARC, announced that he and a group of hardline supporters are taking up arms again, accusing President Ivan Duque of failing to uphold the 2016 accord that ended the fighting.

Luciano Marin, who formerly served as the chief rebel negotiator, condemned the conservative president in a video released early Thursday morning for not taking stronger action in response to the deaths of over 150 former rebels and 500 social leaders since the peace deal was enacted three years prior.

In the aftermath of the peace deal between the FARC and then-Colombian President Juan Manuel Santos’ administration, the former guerrillas have been threatened with extradition to the U.S. for various drug trafficking crimes and many have been killed by paramilitary units in the country.

Mr. Marin, widely known by his alias Ivan Marquez, attributed the death and violence to “the indifference and the indolence of the state.”

Mr. Duque was one of many conservatives critical of the peace deal Mr. Santos forged, a deal that won him the Nobel Peace Prize but one that critics said was too generous to the leftist rebels and failed to give a proper accounting of crimes and atrocities committed in the half-century of civil war.

Flanked by almost two dozen armed guerrilla fighters and fellow FARC leaders, Mr. Marin said that “when we signed the accord in Havana, we did so with the conviction that it was possible to change the life of the most humble and dispossessed.” Mr. Marin insisted Duque government had “betrayed” the peace deal he helped negotiate.

The Colombian government called Mr. Marin’s declaration “a very worrying announcement” and accused Venezuelan socialist President Nicolas Maduro of fomenting unrest in the country. Mr. Marin claimed in the video to be taping from the Colombian jungle, but government officials contended he was actually in Venezuela, given sanctuary by the Caracas government.

“Colombia does not accept threats,” Mr. Duque said in a Thursday afternoon address. “We are not facing the birth of a new guerrilla [movement], but a narco-terrorist band that has the protection of Nicolas Maduro.”

The president said he ordered the country’s Attorney General Fabio Espitia to arrest anyone who appeared in the nearly 30 minute-long video who may be in violation of drug trafficking and weapon possession laws, and threatened to strip the militants of the benefits and legal immunities extended in the peace deal.

By Thursday night, a special tribunal investigating the FARC’s war crimes ordered the arrest of four men in the call-to-arms video, including Mr. Marin and key ideologue Seuxis Hernandez, alias Jesus Santrich.

The Trump administration, which has worked closely with the Duque government in the international pressure campaign against Mr. Maduro, did not respond to a request for comment.

Mr. Santos on Twitter called the protesting rebels a small minority within the FARC and urged continued implementation of his 2016 deal. “The battle for peace does not stop!” he tweeted.

Analysts said that although Mr. Marin’s latest video is serious, it echoes previous complaints by some former FARC rebels over how the peace deal has been implemented.

“His rhetoric is common among factions that have already declared themselves FARC dissidents,” Natalie Adams-Menendez, a research assistant with Stanford University’s Mapping Militants Project, said in an email.

Paul Angelo, a fellow for Latin America studies at the Council on Foreign Relations, said the rebels’ declaration “basically opened the door to a new stage of class warfare.” In the short term, he said, Colombia could see “an uptick in kidnapping of wealthy people or people who are perceived to belong to a landowning and oligarchic class, and an uptick in terrorist incidents in urban spaces where wealthy people and affluent people frequent.”

“The peace process was sort of hijacked by the Duque government because the central government didn’t have enough time to engage in the full implementation of the peace process,” he added.

Speaking to the press Thursday, Miguel Ceballos, the government’s high commissioner to the peace process, said he and his team are entirely committed to the successful implementation of the deal, despite threats from the FARC.

He explained that 90% of the group’s members are still abiding by the existing peace process, and promised support those who continue to participate.

“We acknowledged that they are committed,” he added. Their determination to honor the peace process “is going to be supported by our government.”

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