A U.S. District Court judge yesterday ordered the federal government to pay an estimated $16 million to 324 women who successfully charged the Government Printing Office with sex discrimination -- one of the largest awards ever made in a bias case brought against an employer, public or private.

Judge Charles R. Richey, who set the amount yesterday, had ruled last October that the GPO paid men higher wages then women for the same jobs in its bindery and that the agency deliberately maintained a job classification system that perpetuated sex discrimination.

The case began more than seven years ago when Dorothy M. Thompson, an employe since 1965, went to a group of Washington civil rights lawyers to help a coworker explain a race discrimination complaint. She began talking about her own situation at the GPO, and the lawyers told the sewing-machine operator that she had a basis for a sex discrimination suit.

Eventually Thompson, now 58, gathered four other women in the living room of her suburban Virginia home to discuss conditions at the GPO bindery. The result was a class-action suit that led to Richey's decision.

The judge's award yesterday means that Thompson and 27 other women who operated sewing machines at the bindery in May 1973 will each receive up to $110,000 in back pay, based on Richey's ruling that they were deliberately paid less than men for jobs that required the "same skill, effort (and) responsibility . . ." Thompson could not be reached for comment yesterday.

A lawyer who worked with Thompson at the start of the case recalled that she first noticed differences in the salaries for men and women in the early 1960s, when she worked in a bindery in Kingsport, Tenn. A mother raising two children, Thompson took her complaints to management, the lawyer said, and she was told "a woman will never be paid what a man will be paid."

When the federal Equal Pay Act was passed in 1963, Thompson carried a copy of the law in her purse, and vowed that someday when her family was grown, she would try again.

"For years they told me the big industrial sewing machine I operate was woman's work. But I knew all along I was doing a job same as men, but not getting paid the same," Thompson told a reporter last fall.

In his ruling last October, Richey also said that the GPO bindery's job classification system kept women like Thompson out of better "craft" jobs as bookbinders. Those jobs, Richey said, paid higher salaries and provided promotion opportunities. A four-year apprenticeship program, required for employes who wanted to become bookbinders, was virtually closed to 324 women who, like Thompson, were classified as "journeymen bindery workers," Rickey said.

Those actions, Richey said, amounted to a pattern of sex discrimination, violating Title VII of the Civil Rights Act of 1964.

As a result, Richey yesterday ordered that the government pay 296 other women, working in other low-paying jobs at the bindery, about $3 million in back wages.

Moreover, Richey said, the GPO must continue to pay the women additional money until 50 percent of all bookbinder and supervisory jobs are filled by women.

Attorneys for the women -- the Washington Lawyers' Committee for Civil Rights Under Law and private lawyers David M. Dorsen and Nora A. Bailey -- said yesterday that the provision could ultimately amount to more than $10 million in payments to the women.

Lawyers familiar with such awards said yesterday that employers usually move quickly to adjust their work forces to meet court-ordered requirements. But several lawyers predicted that it could take the GPO 10 years or more to comply with Richey's promotion requirement because there are few jobs openings in the bindery and no new positions in sight.

Richey appointed U.S. Magistrate Lawrence S. Margolis as a "special master" to oversee the computation of the individual awards to the women as well as GPO's compliance with the court order.

Government lawyers yesterday declined to comment on Richey's decision, which they are expected to appeal.

The case was originally brought before Judge Joseph C. Waddy, who died in 1978 before he could issue a formal written opinion. Ironically, Waddy, had ruled against one of the women's major claims in an opinion from the bench before his death. After he died, the case was transferred to Judge Richey and reargued.