The chairman of the Equal Employment Opportunity Commission has rejected the Justice Department's internal management plan for hiring and promoting minority, female and handicapped employes, saying the department did not include goals and timetables.

The rejection accentuates a philosophical confrontation between two agencies traditionally involved with ensuring equal opportunity in the work force. Justice has opposed numerical goals since President Reagan took office; the EEOC has favored them for federal workers.

This is the second time the EEOC has rejected an element of Justice's plan. However, EEOC Chairman Clarence Thomas has no authority to take Justice to court; his weapons are limited to talk and appeals to the White House.

William Bradford Reynolds, assistant attorney general for civil rights, issued a statement yesterday saying: "As is customary with the EEOC, they have apparently communicated with the press before communicating with the attorney general. In light of that, we are in no position to respond . . . . In due time we will provide an answer."

In a July 19 letter to the EEOC, Attorney General William French Smith specifically ruled out the use of numerical goals in the department's hiring plan. "In spite of our best intentions to the contrary," Smith wrote, "such goals often become . . . quotas by operating to give preference in the hiring process to applicants because of race, sex, religion or handicap. That is discrimination and that is wrong."

French's letter began with the salutation "Dear Clarence," and was signed "Bill." The EEOC chairman began his Sept. 2 response with a more distant "Dear Attorney General Smith" and signed it with his full name. In closing his letter, Thomas said, "use of goals in federal employment is presently required, has been required for some time and is necessary for this commission to carry out its responsibilities . . . ."

As of Oct. 1, 1982, about 27 percent of Justice's 54,877 employes were minority-group members; 39 percent were women. Both figures were above the government-wide average; the minority-group figure also was above the national civilian average, but the percentage of women employes lagged slightly behind the national civilian average.

But Justice's plan, according to Thomas, was deficient because it offered no standards for determining whether minorities and women are under-represented in certain job categories.

"Absent this information, neither the EEOC nor Congress can know whether increases in the employment of minorities or women, such as the ones you cite . . . , represent an improvement in the department's equal employment opportunity efforts or merely reflect the addition of more minorities and women in job categories where they are already over-represented," Thomas said.

The ratio of Justice employes with so-called "targeted disabilities"--including long-term impediments to mobility, speech, sight or hearing--was less than half the average in the federal work force, according to EEOC figures. In his letter, Thomas said that while the ratio at Justice improved slightly in the past fiscal year, there still was a net decrease in the number and percentage of disabled individuals working there.

While rating Justice's progress in this area in the past year as "satisfactory," Thomas went on to say: "The entire federal work force is so severely under-represented in this disability category that I am sure you understand why we cannot condone decreasing representation. We must look to agencies to increase their representation on a steady, continuing basis and to commit themselves to do so through setting flexible goals."