The Defense Department, under pressure from congressional investigators, has scrapped a training manual that instructed polygraph examiners to assess the sexual preferences and union, religious and racial associations of persons seeking security clearances.

Trainees at the department's Polygraph Institute at Fort McClellan, Ala., were told in the manual to be "meticulous" in determining whether subjects were members of such ethnic organizations as Polish-American clubs and Japanese community clubs and to explore the degree of blacks' participation in the NAACP.

A list of sample questions contained in the 60-page guide included: "Have you ever received sexual stimulation in a crowded area?" and "Have you ever been a party to an abortion?"

Congress, reacting to a series of spy scandals, has authorized the Defense Department to conduct polygraph tests over the next two years for 11,000 officials with access to sensitive classified documents. But the Pentagon was specifically directed to limit the tests to counterintelligence purposes.

The manual, drafted in February 1984 at Fort McClellan, was designed to "provide the student with a comprehensive summary of personnel screening procedures for future use in field situations," according to the introduction.

Last month, however, the Army, which runs the training center, declared the manual "no longer valid" and ordered it destroyed. Pentagon counterintelligence director John F. Donnelly, in a memorandum Nov. 27, called the contents "inappropriate and in direct violation of the letter, spirit and intent" of the polygraph program.

Donnelly said he was responding to a General Accounting Office investigation, which had criticized the training center for exceeding the counterespionage purpose of the polygraph program.

House Government Operations Committee Chairman Jack Brooks (D-Tex.), a critic of the polygraph program, said yesterday the Pentagon's training operation displayed an "utterly unprofessional attitude" and urged Congress to reject the proposal for permanent authority to conduct such screening.

Use of polygraph tests has been a recurring issue in the Reagan administration. Last month, Secretary of State George P. Shultz threatened to resign if required to take such a test after the president ordered them for thousands of officials.

Defense officials, in their request for congressional authority to conduct polygraph tests, have pledged to restrict their screening to counterintelligence topics, not life-style or personal matters.

But the manual, known as Lesson Plan for Conduct of Personnel Screening Polygraph Examinations, instructed examiners to delve into the most intimate affairs of their subjects, asking such questions as:

*"Are you divorced?"

*"Has any member of your family been an alcoholic?"

*"Have you ever owed a bar bill?"

*"Have you engaged in sex acts with an animal?"

*"Have you ever consulted a psychiatrist?"

*"Do you have foreign pen pals?"

*"Do you belong to a professional organization?"

*"Have you ever belonged to a lodge?"

"Such questioning does not fit the definition of counterintelligence questions offered by the department in selling its polygraph-screening program to Congress and does not comply with the authority Congress granted for a limited counterintelligence test program," Brooks said.