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In a brief hearing before US District Judge Alvin Hellerstein, Maduro, 63, spoke via an interpreter and insisted he was innocent, saying he remained Venezuela’s president.
The judge cut him off as the proceedings moved on.
Cilia Flores, Maduro’s wife, also entered a not-guilty plea.
The next court date was set for March 17.
Outside the courthouse, protesters both for and against Maduro gathered as the hearing unfolded.
Maduro and Flores were transported from a Brooklyn detention facility to Manhattan under heavy guard, with Maduro restrained and dressed in prison clothing as the judge outlined the allegations and advised the pair of their right to notify the Venezuelan consulate.
US prosecutors allege Maduro oversaw a cocaine-trafficking network that worked with violent groups including Mexico’s Sinaloa and Zetas cartels, Colombia’s FARC rebels, and Venezuela’s Tren de Aragua gang.
He faces four criminal counts, including narco-terrorism, conspiracy to import cocaine, and possession of machine guns and destructive devices.
Maduro has long rejected the claims, arguing they are a cover for US ambitions linked to Venezuela’s vast oil reserves.
In Caracas, Delcy Rodríguez, Maduro’s vice president, was sworn in as Venezuela’s interim president, offering supportive remarks about Maduro while giving no sign she would directly confront Washington over the capture.
The Wall Street Journal reported that a recent US intelligence assessment judged Rodríguez best placed to run a temporary administration in Maduro’s absence, while opposition figures such as Nobel Peace Prize winner Maria Corina Machado and former presidential candidate Edmundo González would struggle to gain legitimacy.
The report also said Rodríguez, alongside the interior and defence ministers, was viewed as among the few leaders capable of maintaining order inside a government dominated by ideological opponents of the United States.
Meanwhile, senior officials from Maduro’s 13-year-old administration continued running the oil-producing country of around 30 million people, oscillating between defiance and hints of possible cooperation with Trump’s team.
Rodríguez’s brother, Jorge Rodríguez, was reappointed president of the largely pro-Maduro National Assembly on Monday and vowed to use every available mechanism and forum to push for Maduro’s return.
Trump, speaking to NBC News, said the United States was not at war with Venezuela, describing the campaign as a fight against drug traffickers.
He dismissed talk of a rapid vote, saying Venezuela’s problems would need to be addressed before any election could be held, and called a 30-day timetable unrealistic.
The dramatic seizure intensified scrutiny at the United Nations.
The UN Security Council debated the implications of the operation, which was condemned by Russia, China, and leftist allies of Venezuela.
UN Secretary-General Antonio Guterres raised concerns about potential instability and questioned the legality of the strike, which Reuters described as the most striking US intervention in Latin America since the 1989 Panama invasion.
The report said US Special Forces entered Caracas by helicopter on January 3 and captured Maduro during the raid.
Maduro’s lawyer, Barry Pollack, said he expected extensive litigation over what he called his client’s military abduction, adding that Maduro was not currently seeking release but might do so later.
Flores’ lawyer, Mark Donnelly, said she had been injured during the events surrounding her arrest and asked for medical examinations.
US prosecutors first indicted Maduro in 2020, and an updated indictment made public on Saturday added new details and additional co-defendants, including Flores.
Washington has viewed Maduro as illegitimate since his claimed victory in a 2018 election dogged by allegations of serious irregularities, while some international-law experts have questioned whether the raid breached the rules-based order.
Trump has openly linked the upheaval to energy goals.
He said aboard Air Force One on Sunday that US oil companies would return to Venezuela and rebuild the sector, and he suggested the United States could subsidise the effort, claiming it might be completed in under 18 months.
US oil shares rose on Monday on expectations of access to Venezuela’s reserves.
CBS News, citing two unnamed sources, reported that representatives of Exxon Mobil, ConocoPhillips and Chevron were expected to meet Energy Secretary Chris Wright on Thursday.
A Reuters/Ipsos poll found that about one-third of Americans supported the attack on Venezuela that toppled the country’s leader.
Reuters