A judge declared yesterday that The New York Times "sanitized" the files it surrendered in the Doctor X murder case.He refused to relieve the paper of a $5,000-a-day fine until it orders jailed reporter Myron A. Farber to turn over his notes.

"The files of The Times were clearly and unequivocably sanitized," Bergen County Superior Court Judge Theodore Trautwein said. "I don't know whether there was a break-in or who did it. But it lies at the feet of The New York Times."

As a result of the paper's reporting, Dr. Mario Jascalevich is on trial, accused of killing three hospital patients with a muscle relaxant drug, curare.

In New York, publisher, Arthur Ochs Sulzberger responded: "The unfounded attack on the integrity of The New York Times is a graphic example of the appalling state of justice with which The Times has been confronted since the Dr. Jascalevich trial began.

"Dismayed that The Times' files contained no information of relevance to the case - something, by the way, we had told the court before - Judge Trautwein then accused The Times of 'sanitizing' its files before turning them over. This is flatly untrue."

Reporter Farber, jailed since Aug. 4, says his notes are protected by the freedom of speech provision of the Constitution and by a New Jersey "shield" law which protects reporters from revealing sources.