A 20-month study of federal agencies' handling of employe discrimination complaints has concluded that the process is seriously flawed, with complaints taking years to process, agencies plagued by an "intractable conflict of interest" in assessing possible misconduct by their officials, and employes in charge of handling complaints ill-informed about the law.

The survey, scheduled to be presented today to a House Government Operations subcommittee, concludes that major changes are warranted, including taking responsibility for investigating and deciding discrimination claims away from the agencies. More than 18,000 federal workers annually file formal complaints of discrimination.

The Washington Council of Lawyers, a voluntary bar association including many attorneys who have represented federal workers in such cases, conducted the study at the request of the Government Operations subcommittee on employment and housing.

The group focused on the Department of Health and Human Services, the Department of Agriculture, the U.S. Postal Service and the Veterans Administration.

Although federal agencies' handling of discrimination complaints has been criticized for years by civil rights lawyers, federal employe unions and others, the council study provides empirical evidence to support such views.

"No one before has done a study of the causes for this or documented that it indeed has happened," said council president Joseph M. Sellers. "The significance of this . . . is that we've attempted to do some documentation of the existence of these problems."

Agency officials generally defended their performance, and attributed much of the problem of delays to the Equal Employment Opportunity Commission, which handles the final stages of the process.

"I think the agencies can view these things fairly objectively," said Peter Garwood, in charge of complaint processing at the Postal Service.

"As far as the conflict of interest and the training part of it, I wouldn't agree with their conclusion at all," said Earl C. Hadlock, deputy director of personnel at the Agriculture Department. As to delays, he said, "It's a process that you can't generally say takes too long. We're always trying to make it shorter."

The council surveyed 350 officials responsible for administering the equal employment opportunity process, interviewed many at length, and reviewed the agencies' statistics.

Among the findings:Although discrimination claims are supposed to be processed within 180 days, that goal is rarely met, in part because EEO offices are underfunded, understaffed, and "typically relegated to a lower status" in an agency, and because the "alleged discriminating official" must approve any informal resolution or settlement.

In fiscal year 1985, the average processing time for a complaint to be decided was 1,110 days at the Veterans Administration, 1,105 days at the Department of Agriculture, 771 days at the Department of Health and Human Services and 443 days at the Postal Service. Agencies' dual roles as the judge of discrimination complaints at the administrative stage and the ultimate defender against them in court creates "an intractable conflict of interest that substantially impedes the operation and effectiveness of the EEO administrative process."

One staff lawyer told the council he viewed his role "as an adversary of the complainant"; another official described the "built-in incentive to find no discrimination" because such a finding means more work. When this official was planning to issue a finding of discrimination against a politically well-connected official, he said, the decision was delayed for eight or nine months and senior officials rewrote the decision to soften the language. There was "unanimous agreement" among those interviewed "that the employes involved in every state of the EEO process do not have the skills or the knowledge of the law that they need to administer the process."

The council recommended that fact-finding and assessment of claims be conducted by "a single team of highly trained staff who are fully independent of the agencies against which the EEO claims are pending" and said the EEOC is a "likely candidate" to play that role. However, it said, the EEOC's "poor record" in handlng private-sector complaints "counsels caution in entrusting to that agency substantial new responsibilities."