Thornburgh Cites Risks in CIA Trial : Iran-Contra: The attorney general says ‘national security’ could be damaged in prosecuting a former station chief.

In an unprecedented move that could scuttle the case, Atty. Gen. Richard L. Thornburgh told a federal judge today that “national security” would be damaged if classified information is used at the Iran-Contra trial of a former CIA official.

Thornburgh filed a classified affidavit at a pretrial hearing for Joseph Fernandez, the former CIA station chief in Costa Rica. U.S. District Judge Claude Hilton ordered the hearing resumed on Friday.

Appearing for the Justice Department, Deputy Atty. Gen. Ronald Noble said various intelligence agencies object to some evidence that Fernandez wants to use in his defense.

Thomas Wilson, the lawyer for Fernandez, told Hilton that “the indictment must be dismissed” if Thornburgh’s affidavit concerns “CIA facilities in Latin America” and certain CIA projects that he did not identify.

“I think the statute is clear,” Wilson said, and information about CIA facilities and projects is “indispensable” to the Fernandez defense.

A lawyer for the office of special prosecutor Lawrence E. Walsh criticized Thornburgh for “having waited four months” before making his move under the Classified Information Procedures Act.

“We deplore the fact that the attorney general for the first time has filed an affidavit to protect fictional secrets which could prevent the trial of a former high-ranking CIA official,” Walsh said in a statement.

About an hour after the hearing, Thornburgh’s spokesman, David Runkel, told reporters at the Justice Department that Thornburgh’s action was not based on political concerns, such as exposure of White House knowledge of Fernandez’s allegedly illegal activities.

“The only consideration was national security,” Runkel said, adding that the White House had been told of Thornburgh’s decision to file the affidavit.

Noble, meeting with reporters, refused to discuss any aspect of the Thornburgh statement to the court but raised the possibility that Fernandez could be tried on charges less objectionable to the intelligence community after further negotiations with Walsh.