Eleven high officials and agents of the Church of Scientology, including the wife of the founder, L. Ron Hubbard, were charged here yesterday in an allegedly widespread conspiracy to plant spies in government agencies, steal official documents and bug government meetings.

Much of the evidence outlined against the church's officials in the 28-count criminal indictment appears to be based on the church's own internal memorandums and other documents. The memorandums directed church operatives to "use any method" in its battle with the government.

Church spies were used, according to the indicment, to find out about Scientology's tax-exempt status, rumage through government files to get information on the church and on persons or groups it perceived to be its "enemies." They were also used as an "early warning system" to protect Hubbard from government acrunity, the indicment alleged.

Assistant U.S. Attorney Raymond Banoun asked the arrest warrants be issued immediately for the church's Worldwide Guardian, Jane Kember, and her chief aide, Morris (Mo) Budlong, in England, and said extradition proceedings against them would begin soon.

The other indicted church members, including Commodore Staff Guardian Mary Sue Hubbard, the wife of the founder, are scheduled to appear in federal court here at 1 p.m. Thursday. Banoun said he had been assured by the attorneys for those church members that they would appear as scheduled.

A spokesman for the church, which is described in its literature as an "applied religious philosophy which believes that man is a spiritual being and is basically good," said the indicment is the latest episode in nearly 30 years of harrasment against the church by government agencies.

". . . If justice is done our members will be exonerated as any have been who fought for religious freedom against government oppression throughout history," said the church's Deputy U.S. Guardian Henning Heldt, who was among those indicted yesterday.

The indicment charges that the church's "guardian office" included a bureau that "was assigned the responsibility for the conduct of covert operations," and that all of those charged with crimes were members or officials of the bureau.

The church said, however, that the guardian office is the "social reform arm of the church." Church attorney Phillip J. Hirshkop described the indicments as part of a "bureaucratic vendetta against Scientology" and said "any actions attributed to church members is a direct result of government misconduct."

The 42-page indicment, one of the longest returned by a jury here in recent memory, climaxes a sometimes bizzare investigations that began when two Scientology operatives were confronted by FBI agents in June 1976 in the federal courthouse here after employes became suspicious of their regular nighttime presence.

The two men, who had entered the building by using allegedly forged Internal Revenue Service passes, were allowed to leave. Unknown to the agents at the time, the two were part of the alleged undercover Scientology operation and had been assigned to the courthouse to enter offices there and copy documents, according to the indictment.

The two men fled to California and with Scientology officials concocted a cover story to explain their presence in the courthouse, according to the indicment. One of them, Gerald Bennett Wolfe, returned to the courthouse here a year later and pleaded guilty to using fake IRS credentials.He was placed on probation.

The other alleged courthouse intruder, Michael Meisner, had been hidden by the church in Los Angeles for more than a year, having had his appearance changed and using a false name, according to the indicment. When he threatened to return to Washington against the church's will, he was held under guard and his "bodyguard crew" was told to "gag, handcuff" him if necessary, the indicment continued.

Meisner escaped from his guards in June 1977 and came to Washington , where he agreed to plead guilty to a five-year felony. He is the government's main informant against the church, and is being held under tight security.

When he came to Washington, Meisner outlined the alleged Scientology infiltration plot in great detail to federal agents and they obtained a search warrant for the church's headquarters in Los Angeles and Washington. Those warrants were executed on July 8, 1977, and resulted in a massive seizure of church documents that reported outlined a campaign of harrasment and infiltration directed against numerous individual critics of the church as well as against government officials and agents.

According to the indictment returned yesterday, the alleged criminal conspiracy by the church began on Nov. 21, 1973, when Kember directed Heldt and his staff to obtain all Interpol (the international police organization) documents concerning Scientology and Hubbard.

Meisner was brought into the plot in mid-1974 when he was told by a superior, Cindy Raymond, that he was to help her place a "loyal Scientology agent" as an IRS employe in the District of Columbia, the indictment stated. Raymond, identified as the national secretary of the church's U.S. information bureau, was among those charged yesterday.

Kember issued another order, known in church terminology as Guardian Program Order 1361, on October 1974, directing the infiltration of the tax division of the Justice Department, according to the indictment.

Two of those who received that order, Deputy Guardian-Information U.S. Richard Weigand and Deputy-Deputy Guardian U.S. Duke Snider, also were charged in yesterday's criminal conspiracy.

Within days of that order, according to the indictment, three Scientology agents planted an electronic listening device or "bug" in an IRS conference room here and "recorded an IRS meeting concerning Scientology's application for tax-exempt status and related matters." Less than 18 days later, Wolfe was employed as a clerk-typist at the IRS.

One of the agents who allegedly planted the bug, Mitchell Herman (also known as Mike Cooper), also was charged yesterday. At the time of the alleged offense, his title with the church was Branch 1 director of the Guardian's office, D.C.

Once Wolfe was in place at IRS, the indictment charged, he began stealing IRS documents that would then be flown out to the church's top officials in the Los Angeles area.

Among the IRS offices from which Wolfe stole documents were the chief counsel's office, that of an assistant IRS commissioner, and other lawyers, according to the charges.

In May 1975, Wolfe also turned his attention to the tax division of Justice and stole documents from the offices of three attorneys there as well, the indictment charged.

Mary Sue Hubbard then told Kember and Heldt on May 27, 1975, to "use any method at our disposal to win the battle and gain our nonprofit (tax) status," according to the charges. Gregory Willardson, then the Church's Information Bureau Branch I director in the United States, soon wrote a letter to Meisner asking him to prepare a plan to get further IRS documents, the indictment stated. Willardson also was charged yesterday.

Six months later, an order known as the "Early Warning System" was issued by the church hierarchy, and it was "designed to protect the 'personal security' of" L. Ron Hubbard, the indictment stated.

"The order called for the infiltration of government agencies which had power to subpoena or bring suits against Hubbard or which would possess advance warning of such subpoenas or suits," the indictment continued.

The indictment said that as the plot continued:

A Scientologist, Sharon Thomas, was placed in a job at the Justice Department as a secretary and stole documents from an attorney's office there.

Guardian's office officials met in Los Angeles to discuss the burglaries, the infiltrations, and documents obtained by Scientologists.

Meisner and Wolfe forged IRS credentials and used them to break into the offices of Assistant U.S. Attorney Nathan Dodell at the U.S. Courthouse here.

Meisner and Wolfe broke into the offices of Associate Deputy Attorney General Togo G. West Jr. and Special Assistant Attorney General for Administration John F. Shaw and stole documents from both places.

Even after the charges were filed against Wolfe and Meisner in connection with the alleged illegal use of IRS credentials, the church tried to implement what it called "Project Troy." That project reportedly called for the installation of a permanent "bug" in the IRS chief counsel's office, and was approved by Heldt on Dec. 20, 1976.

In May 1977, the church again called for the infiltration of the U.S. Attorney's Office in Washington "for the purpose of obtaining information about any potential legal action against L. Ron Hubbard."

All of the defendants except Wolfe and Thomas are charged with one count of conspiracy to steal government documents, burglarize governments offices, intercept oral communications and forge government passes. 10 counts of theft of government property, one count of intercepting oral communications: 10 counts of burglary, and one count of conspiracy to obstruct justice, to obstruct an investigation, to harbor a fugitive, and to make false declarations before a grand jury.