The additional charges, brought last Thursday, significantly expanded the US criminal case against Maduro, 63, and Flores, 70.
They previously pleaded not guilty to charges that they abused their power to help drug traffickers ship cocaine.
Maduro and Flores, captured by the US military in a January raid ordered by President Donald Trump and flown to New York, entered their pleas at an arraignment before US District Judge Alvin Hellerstein in Manhattan federal court.
They wore tan prison garb and were shackled at the ankles during the hearing.
When Hellerstein asked for his plea, Maduro said the accusations had been made previously and were false.
"I have seen it in its entirety, Judge Hellerstein," Maduro said, referring to the indictment.
"I reject this document in its entirety."
The judge cut Maduro off as he spoke and said a plea of not guilty would be entered on his behalf.
Flores said, "I am completely innocent. I am not guilty."
Maduro and Flores are not accused of personally carrying out any acts of torture.
They would each face a mandatory minimum sentence of 50 years in prison if convicted on all charges.
Hellerstein postponed the trial start date by two weeks to June 14, 2027, due to the new charges.
Prosecutors with the Manhattan US Attorney's office say Maduro directed Venezuelan officials to torture opposition politicians and military personnel accused of plotting against him to maintain power in the country.
In one alleged incident described in the indictment, Maduro in 2014 directed officials to kidnap military personnel to draw information out of them about possible dissidents, and told officials to "squeeze them harder" when some remained defiant.
Flores agreed with the plan in the meeting and dismissed a suggested alternative plan to glean information by infiltrating the ranks, according to the indictment.
Relations between Maduro, a socialist, and the United States were tense during his 13 years in power leading the oil-rich country.
Successive US administrations imposed sanctions on top Venezuelan officials and key state companies, citing alleged human rights violations, corruption and election-rigging.
Maduro accused the United States of seeking his ouster to gain greater control of the country's natural resources.
10°C