Andrew Brunson, who faces up to 35 years in prison, was also said to be "devastated" to learn he was being moved to a prison described as "extremely grim" by his supporters.
First detained in October 2016 as part of a visa investigation, he was later accused of involvement with two organisations Turkey considers to be terrorist in nature and behind a botched coup earlier that year.
Addressing a judge in the Mediterranean city of Izmir, the 50-year-old from North Carolina was quoted by Reuters news agency as saying: "I do not accept the charges mentioned in the indictment.
"I was never involved in any illegal activities."
Supporters of Andrew Brunson, a missionary who had spent 23 years in Turkey, say he has been targeted with false accusations specifically because of his Christian faith.
In a statement released on Tuesday, the US State Department said: "We have seen no credible evidence that Mr Brunson is guilty of a crime and are convinced that he is innocent."
"Turkey is a state bound by the rule of law, and we have faith in the Turkish people's commitment to justice.
"We hope that the judicial system in Turkey will resolve his case in a timely, fair, and transparent manner."
Brunson is being supported by Washington DC-based advocacy agency the American Center for Law and Justice.
Speaking after a judge decided to halt Brunson's trial for three weeks and keep him in custody, the centre's chief counsel Jay Sekulow said: "Instead of being returned to the prison where he had been held most recently, the judge ordered Pastor Andrew to be taken back to an overcrowded and extremely grim prison where he was held initially.
"As you can imagine, the news is devastating to Pastor Andrew and his family."
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