The 49-year-old, who also has Irish, Canadian and British citizenship, was held in December last year for allegedly receiving state secrets. He risks up to 20 years in prison if convicted.
Appearing in court in a dark sweater and jeans, he told AFP he believed he was being held as a hostage for a potential prisoner exchange.
During the hearing, Whelan asked for the prosecutor and judge to be removed from the case.
"Evidence that I provided has been ignored... questions of law are always decided in favour of the prosecutors and the FSB (security service)," he told the judge.
UK intel files shed new light on famed Cold War spy cases
The requests were rejected and the judge announced his detention would be extended until December 29.
Whelan, a former US marine, maintains he has been framed and that he took a USB drive from an acquaintance thinking it contained holiday photos.
He has used earlier court hearings to appeal to journalists in English, saying that he is being mistreated in prison, not given full translations of documents and rarely given access to his lawyer.
Whelan's Russian lawyer Vladimir Zherebenkov said in September that the investigation into his case is now completed and Whelan and his lawyers are reading the files.
The US House of Representatives on Tuesday passed a resolution calling for Whelan's release.
His Russian lawyer has said he needs an operation on a hernia. His brother David said in a statement Tuesday that his "medical condition continues to be of great concern."
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