Secretary of State George P. Shultz, in a highly unusual and emotional dissent from administration policy, said yesterday that he would resign if required to submit to a polygraph examination as thousands of government officials must under a directive signed recently by President Reagan.

"The minute in this government I am told that I'm not trusted is the day that I leave," Shultz declared in discussing what he called his "grave reservations about so-called lie detector tests."

In answer to questions, he said that he would submit to such a test if ordered to do so, but only "once," and that he would then resign because of the lack of trust implied by such a requirement.

Shultz was reported to have expressed strong opposition within administration councils to Reagan's order Nov. 1 that polygraph examinations be administered to U.S. officials having access to "sensitive compartmented information" of a secret nature.

Shultz's decision to go public with his objections and with his personal refusal to accept polygraph tests as a fact of his life added a serious new element to the extensive controversy about Reagan's directive.

Shultz has never suggested publicly that he might quit as secretary of state over a matter of governmental policy, and rarely, if ever, in his long career in high office has he spoken publicly in objection to a decision by a president he served.

After Shultz's remarks, the usually close-mouthed Central Intelligence Agency, where Director William J. Casey is reported to be an advocate of polygraphs, telephoned news organizations with a statement supporting the Nov. 1 order.

The CIA said "there is an acute need" to extend "selective" and "careful" use of polygraphs to governmental users of secret information, such as the State and Defense departments.

Polygraphs have been used routinely, extensively and for a long time to screen employes of CIA and the top-secret National Security Agency.

In contrast, they have been used only as a selective and "voluntary" investigative tool at the State Department. Congress has limited a Reagan administration test program of large-scale polygraph screening at the Defense Department to 3,500 exams per year.

Those subject to the Nov. 1 order, according to General Accounting Office data, include at least 4,550 State Department employes and contractors and 122,000 Defense Department employes and contractors.

Reacting in late 1983 to news leaks about U.S. operations in Lebanon, Reagan secretly approved a recommendation from then-national security affairs adviser William P. Clark to give top U.S. officials polygraphs.

The president revoked the order after Shultz and then-White House chief of staff James A. Baker III said they would resign on principle if required to submit to such tests, according to administration officials.

This time, the polygraph requirement was presented to Reagan and justified in White House statements as a "counterintelligence and counterespionage" measure in the wake of several notorious spy cases.

White House spokesman Larry Speakes said in discussing the order after it came to light last Wednesday that it was directed against "both" espionage leaks and news leaks. But a White House official said yesterday that it is "sheer nonsense" to think that it would be used against unauthorized or unpalatable disclosures to the media.

Speakes said last week that the polygraph exams would be conducted "from senior levels on down" under the order, which he assumed would apply to Cabinet members. A White House aide hinted yesterday that Cabinet members might be exempt, saying they "already go through the most stringent background investigation in connection with their confirmation."

Shultz's declaration left in doubt his department's preparations to comply with Reagan's order. Department employes here and in embassies around the world were notified of the presidential order by Deputy Secretary of State John Whitehead last Saturday, while Shultz was traveling in Europe, and were told that a National Security Council task force, including State officials, is studying its implementation.

A senior State Department official said at least two dozen full-time polygraph operators probably will be needed permanently to administer the tests to U.S. diplomats and other department personnel. He added, even before Shultz spoke out, that "a lot of people" at the department are likely to refuse to take the exams.

Shultz declined repeatedly during his recent overseas trip to discuss his attitude toward the order on grounds that it is a domestic matter that should be addressed only at home.

He disclosed his refusal to accept polygraphs while appearing before the media to announce a 12-member advisory committee on South Africa policy headed by former IBM Corp. board chairman Frank T. Cary and former transportation secretary William T. Coleman Jr.

Shultz said the polygraph, in his personal view, is "hardly a scientific instrument" and "tends to identify people who are innocent as guilty and misses at least some fraction of people who are guilty of lying." He added that "a professional spy or a professional leaker" could avoid detection through training.

Therefore, Shultz said, use of polygraphs "as a broad-gauge condition of employment seems . . . to me to be questionable."