For the second time in two weeks, a federal judge has disqualified himself from trying the case of nine members of the Founding Church of Scientology charged with conspiring to steal government documents.

U.S. District Judge Louis F. Oberdorfer removed himself from the case yesterday, citing "personal knowledge" of disputed facts that will be in evidence in the trial.

Oberdorfer was head of the Justice Department's Tax Division from 1961 to 1965, during which time the federal government successfully moved to deprive the Church of Scientology of its tax-exempt status. The defense has moved for dismissal of charges against the defendants, citing "misconduct" -- including the tax ruling -- by the government as one of the grounds.

The government suggested that Oberdorfer should withdraw since he would be in the position of judging his own conduct when ruling on the motion to dismiss the charges.

Two weeks ago, U.S. District Judge George L. Hart Jr. removed himself at the request of the defense when it became clear that a document mentioning Hart would be used by the prosecution in presenting its case Hart had been investigated secretly by the church, a circumstance which he said did not bother him but which other persons might believe would affect his impartiality.

Oberdorfer, in removing himself, cited a provision of federal law requiring a judge to step out of a case if he has "personal knowledge of disputed evidentiary facts concerning the proceeding."