The Church of Scientology used a special filing system with the code name of "Red Box" to conceal any "proof that a Scientologist is involved in criminal activities," according to Scientology documents seized in an FBI raid on church headquarters in Los Angeles last July.

The disclosure of the "Red Box" filing system came at a hearing last month before U.S. District Judge Malcolm Locas in Los Angeles, who is considering a motion by the church to have the search ruled illegal.

Prosecutors disclosed at the same hearing that when the "Red Box" system was discovered during the search, they obtained a search warrant for another California location where additional "sensitive Red Box" documents were allegedly kept by the church. However, by the time FBI agents had arrived at that location, witnesses there told them the files had been hastily removed earlier that day, investigators said.

Documents concerning the "Red Box" filing system were found in file drawers labeled "confessional formularies" at the church's headquarters, according to FBI agents who testified at the hearing and an inventory of documents taken during the search.

The agents also said they had been told before the search that allegedly stolen government files might be kept by the church in "confessional" file drawers "in order to throw . . . of" any searchers who might think the drawers contained religious documents.

The church is under investigation by grand juries in Washington, New York and Tamapa, Fla., for an alleged conspiracy by its highest officials to infiltrate government agencies, steal government documents, wiretap at least one government meeting, and obstruct justice.

A church spokesman in Los Angeles said he would not "cooperate with" specific questions about the terms "Red Box" and "confessional formulary," and called the previously unreported comments "old news."

Instead, the spokesman issued a brief statement saying the federal government was "terrified" by a church program to expose "government crimes and cover-ups."

"They're trying to paint a picture in the press and courts which will further their efforts to cover up their crimes and halt exposes from reform groups such as the Church of Scientology," the spokesman continued.

He said the Justice Department and FBI "are after total freedom to search and seize anything from any group" and that "anything the FBI or government says must be viewed in this context."

The church's attorneys are contending in the Los Angeles hearing that the agents did not follow proper search procedures in searching the church's headquarters. They dropped claims during the hearing that the agents acted in "bad faith," but argued instead that the agents should have looked for specific filing cabinets mentioned in a search warrant affidavit before moving on to a more general search of the desks and cabinets in various church offices.

The agents said during the hearing that, once they entered an office they were about to search, they felt no obligation to follow any set search pattern of the office and its contents. The government argued that the agents had a right to search in the manner they searched and that the search was legal.

A federal judge in Washington ruled last year that the affidavit upon which the warrant for Scientology offices in Los Angeles and Washington was based was too general and therefore the searchers were totally illegal. However, he was later reversed and the hearings have since moved to Los Angeles to focus on the actual manner in which the raids there were conducted.

The discussion of the "Red Box" system came up during a week-long hearing in early June before Lucas, and documents concerning the material were discussed by Lucas himself, church attorneys and federal prosecutors in open court.

The church contends that the search was a general rummaging of files protected by the First Amendment and accompanied by unecessary force by the FBI in breaking open filing cabinets and breaking down doors. The FBI contends the search was carefully limited, and that any force to enter offices or filing cabinets was used only after church members failed to produce keys or engaged in "delay. . . disruptive tactics."

Among the tens of thousands of documents seized in the raids were numerous items marked "Red Box," according to an inventory of the search and FBI testimony.

According to other sections of the inventory listing the seized documents, the material allegedly contained in "Red Box" files appears to include documents on the Atomic Energy Commission, Federal Trade Commision, Internal Revenue Service, numerous large and small police departments across the country, several state and local agencies, the National Security Agency, the Central Intelligence Agency, the Labor Department, the Defense Intelligence Agency, the Drug Enforcement Administration, the department of Navy and Army, and the U.S. Customs Service.

Investigators found that some of the seized file folders marked as containing information on those agencies were in fact empty save for a notation that whatever material had been enclosed had been sent to "Red Box" files, the agents testified.