Lawyers for former foreign minister Ieng Sary "face sanctions" if they do not remove all documents relating to judicial investigations within 48 hours, the court's co-investigating judges said in a press statement.
Ieng Sary, 83, is one of five leaders from the late 1970s regime charged with crimes against humanity and war crimes, but details of the investigation ahead of his trial are kept confidential.
Investigating judges said they needed "to guarantee the protection of privacy of those persons mentioned in the case file and the presumption of innocence, as well as to promote efficiency in investigations."
But the website containing defence filings and letters has also posted a letter to court officials saying that no documents on the site relate to the current investigation of Ieng Sary.
The letter by defence lawyers Michael Karnavas and Ang Udom goes on to allege that judges suppress filings "which may be embarrassing or which call into question the legitimacy and judiciousness of acts and decisions."
Ieng Sary has been rushed to hospital nine times since he was detained by the court in November 2007, and last week had an appeal for release from the Khmer Rouge court delayed after he said he was too ill to appear in court.
As the top Khmer Rouge diplomat, Ieng Sary was frequently the only point of contact between Cambodia's secretive communist rulers and the outside world.
He has denied any involvement in atrocities but he was one of the biggest public supporters of the regime's mass purges, researchers say.
Up to two million people died of starvation and overwork, or were executed, as the 1975-1979 regime emptied Cambodia's cities in its drive to create a communist utopia.
The long-awaited first Khmer Rouge trial started last month when the regime's notorious prison chief, Kaing Guek Eav, better known by the alias Duch, went before the court.