Intensive military interrogation of Marine Sgt. Clayton J. Lonetree in recent weeks, supported by polygraph tests and psychological examinations, strongly indicates that the former guard did not, as earlier believed, arrange for Soviet agents to penetrate the U.S. Embassy in Moscow, according to officials of two U.S. agencies.

The new evidence, considered reliable but not yet conclusive by officials familiar with it, suggests strongly that the security "disaster" of Soviet agents roaming through sensitive portions of the embassy with the cooperation of Marine guards never took place.

The fear that Soviets were allowed into the embassy building after working hours by Lonetree and a coworker, Marine Cpl. Arnold Bracy, was the most sensational aspect of last spring's Marine guard spy scandal. Later, however, charges against Bracy were dropped and the spy charges against Lonetree were changed to delete the accusation that he had helped admit Soviets to the building. Lonetree was subsequently convicted of espionage on other charges related to his contacts with the KGB secret police.

But the State Department, assuming that Soviet spies had penetrated the embassy, has treated even the most heavily guarded facilities in the building in central Moscow as having been compromised. In April, it flew a special secret communications van to the Soviet capital for the visit there by Secretary of State George P. Shultz. Highly classified messages from Moscow continue to be taken by daily courier to Frankfurt, West Germany, rather than transmitted in coded communications.

In the midst of the scandal, the Marine Corps took the unprecedented step of recalling the entire 28-member Moscow guard detachment, and the State Department authorized the spending of millions of dollars to replace sophisticated communications facilities in Moscow and overhaul other aspects of the chancery building on an emergency basis.

Officials said there is no relationship between the U.S. Marine Guard security breaches in the U.S. Embassy and the alleged bugging of a new U.S. Embassy building which has been under construction nearby for several years.

Lonetree, who turned himself in to the Central Intelligence Agency station chief in Vienna last December for having contact with a KGB agent in Moscow, never said he had allowed Soviet agents into the embassy and denied it whenever it was put to him, according to his civilian attorney, Lawrence D. Cohen of St. Paul, Minn.

The alarm bells over Soviet penetration were touched off in mid-March when Bracy, who had been summoned for interrogation about his service in Moscow, signed a statement at Twentynine Palms, Calif., saying he had cooperated with Lonetree in permitting Soviet agents access to sensitive areas and cryptographic equipment in the Moscow embassy.

But then Bracy recanted the statement, accusing his Naval Investigative Service (NIS) interrogators of coercing him into making false declarations.

Nevertheless, many senior officials in the State Department and U.S. intelligence agencies continued to operate under the belief that Bracy's original statement had been true, and that he recanted under the advice of lawyers to protect himself.

Officials have confirmed, however, that no listening devices or other physical signs of entry into the existing chancery have been found.

A senior State Department official recalled that the department went into "a frenzy" at the news of the presumed Soviet penetrations. A Marine Corps official said "everybody was shaken" at reports that Lonetree had provided the names of CIA officials in the embassy to the KGB for pay, but that the word from Bracy of Soviet penetration caused "everybody to go to general quarters" (battle stations).

In March, Lonetree, already facing charges of espionage, was charged with conspiring with Bracy to allow "unauthorized personnel from the USSR" in the embassy in Moscow for periods of one to four hours. Similar charges were filed against Bracy.

About a month later all charges against Bracy were dropped bedause of lack of corroboration and the charges against Lonetree were changed to omit any mention of possible Soviet penetration of the embassy.

Lonetree was convicted at his military court-martial in August on 13 charges of espionage and related offenses. He did not testify and in a brief statement after his conviction, said nothing about admitting Soviets to the embassy. Sentenced to 30 years' imprisonment, he later accepted a government offer to cooperate in new "damage assessment" interrogations in return for a reduction of at least five years in his sentence.

These interrogations have been taking place since Oct. 13 at the U.S. Navy Yard here, with a single interrogator asking questions of Lonetree while his military attorney and officials of the CIA, NIS, the Marine Corps and at times State Department watch by closed-circuit television.

Starting last Monday, Lonetree was subjected to polygraph examinations voluntarily. As the interrogation reports and polygraph results, plus the observations of psychological experts assigned to monitor the questioning, have circulated among senior officials, the belief has grown that Lonetree is telling the truth.

Following the interrogations, which are expected to continue for several weeks, the Marine Corps will rule on a further reduction of Lonetree's now 25-year sentence, which some U.S. security officials are saying is too harsh. After that, attorneys for the 26-year-old Marine are expected to begin formal appeals of his conviction and sentencing.