"Something is not right, we just don't lose things like that," judge Anita Leeser told Dutch news show NOVA late yesterday.
"I find it bewildering that people lose files with a political goal, especially if it is on request of the CIA. It is unheard of," she added.
Khan, who admitted in 2004 that he had leaked nuclear secrets to Iran, North Korea and Libya, worked as an engineer in the Netherlands at Urenco, an uranium enrichment plant in the 1970s.
In 1983 he was sentenced in absentia, by judge Leeser, to four years in prison for stealing nuclear secrets about uranium enrichment. On appeal the verdict was quashed because of procedural errors and the Dutch government did not pursue the matter any further.
A month ago former Dutch prime minister Ruud Lubbers said Khan was let go at the request of US intelligence services.
Leeser said that when she heard Lubbers, the disappearance of Khan's files at the Amsterdam court's archive fell into place for her.
She has asked to see the Khan case files several years ago but they had disappeared from the archives.
"Now I think somebody lost the files on purpose ... I think that there was some political influence at play nationally and internationally," she said.