Nicolás Maduro insisted on Thursday during an appearance in a New York court that torture allegations in a rewritten drug trafficking indictment against the deposed Venezuelan president and his wife were “false accusations”.

Maduro, shackled at the ankles, was brought to court to face the new charges accusing the couple of leading a state-sponsored campaign of repression that tortured scores of victims, including three Americans.

Judge Alvin K Hellerstein entered a not-guilty plea on behalf of Maduro and his wife, Cilia Flores. They were seized from their Caracas home by the US military in a night-time raid in January.

Hellerstein announced that he was entering the plea on behalf of Maduro after Maduro twice responded to the judge’s request to enter a plea by criticizing the indictment, saying it contained “false accusations and false testimony”. Maduro spoke through an interpreter.

Attorney Barry Pollack said when the charges were announced last week that Maduro, 63, denied them and “looks forward to his day in court”.

According to the rewritten indictment, Maduro oversaw a violent torture system that beat, asphyxiated and delivered electric shocks to its victims. He is accused of personally recommending torture methods, receiving updates on specific victims’ treatment and threatening to kill one prisoner’s child as a form of psychological torture.

Flores, 70, a former attorney general, helped develop the repressive system and ordered the torture of some specific people, the indictment alleges.

When she was asked to enter a plea, she said through an interpreter: “I am completely innocent. I am not guilty.”

Maduro, who served as Venezuela’s president from 2013 until his capture in January, has been under investigation for years by the international criminal court over allegations of crimes against humanity, tied to his crackdown on opponents. He has always denied wrongdoing.

Prosecutors told the judge during the hearing that lawyers on both sides want the trial date moved from 1 June to 14 June.

Torture is a crime under international law and can be prosecuted outside the country where the abuse occurred and regardless of the victims’ nationality. But the prosecution of foreign officials in the US is exceedingly rare, having been tried only a few times, including against the son of the former Liberian president Charles Taylor, Russians responsible for war crimes in Ukraine and a former prison warden in Bashar Assad’s Syria.

Earlier this year, Maduro and his wife pleaded not guilty in the US drug case, which said they conspired to flood the US with cocaine. Their attorneys say the case should be dismissed on immunity grounds because they were the leader and first lady of a foreign country.

The revised indictment covers allegations of torture stretching back to Maduro’s ascent to power in 2013, when he took over as president from his mentor Hugo Chávez, who died of cancer that year.