The Agriculture Department has decided to rehire a black employe it fired last spring in a civil rights dispute, but still has taken no final action in the case of a nutritionist whom its Extension Service has tried to dismiss.

Vertis M. Stovall Jr., who was fired by the Animal Plant Health Inspection Service (APHIS), said yesterday that he has been told to return to the department next week, with a promise of back pay and a promotion that earlier had been denied him.

But the status of Edith Thomas, a nutritionist who is the highest-ranking black woman employe in the Extension Service, remains unclear. The service backed away from plans to fire her in May, and suspended her pending the outcome of an appeal hearing.

The service agreed in June to return Thomas, who has a doctorate in nutrition, to a temporary new assignment. But the hearing examiner's recommendations, which had been promised by June 6, apparently have not been made.

Meanwhile, Thomas' attorney, Joseph D. Gebhardt, said that the department has rejected nine of the 10 discrimination complaints that she filed against the Extension Service at the time of the agency's attempts to fire her.

"It is shocking to me that the highest officials of the Extension Service could issue a 65-page letter denying discrimination in the Edith Thomas case," he said. "They admit there were problems, but they gloss them over . . . . All of these complaints had been decided in Dr. Thomas' favor during our earlier talks about a settlement."

After lengthy internal wrangling with the Extension Service over its moves against her, Thomas publicly charged that the agency had denied nutrition assistance to low-income minority groups that had sought her advice. She also charged that the dismissal efforts resulted in part from the service's refusal to allow her to work with the groups.

Criticism of the USDA by members of Congress and civil rights groups over the Stovall and Thomas cases played a part in Secretary Richard E. Lyng's issuance last month of a no-discrimination order to all departmental officials. Lyng warned that officials who ignored his order could be fired, and he assigned Peter C. Myers, deputy secretary, as enforcer.

Four House subcommittees have directed Lyng to provide information about civil rights and equal opportunity enforcement at USDA. In a letter to Lyng last week, Rep. Don Edwards (D-Calif.), chairman of the subcommittee on civil and constitutional rights, asked for a briefing on 11 cases of discrimination alleged by USDA employes.

Among the 11 were the Stovall and Thomas cases. Edwards said another of the cases, a complaint by Frank Scott, a former Farmers Home Administration district director in California, involved allegations that FmHA officials had removed or destroyed documents from the case file.

Edwards said his staff had been told that an investigator's finding of discrimination in the Scott case had been reversed by FmHA chief Vance Clark.

"I am sure you share my concern about the seriousness of these allegations and would agree that such action would be totally inconsistent with the spirit of your strong statement on civil rights," Edwards said in a second letter.

Stovall was dismissed by APHIS last spring on the ground that he had misrepresented a commercial publishing firm's work as his own and caused USDA unnecessary expense in giving overtime pay to a typist to photocopy the material.

But Stovall, who had a letter from the publisher granting permission to use the material, charged that the firing was retaliation for his participation in an official USDA review that found his agency in violation of civil rights laws.

APHIS subsequently agreed to develop a new enforcement plan. Stovall said that his new assignment will be in the U.S. Forest Service, where he will continue as a personnel management specialist.