A federal judge who ruled yesterday that a black employe's denial of tenure by the Agency for International Development was "racially motivated," ordered the agency to reinstate him and eliminate racially biased employment practices.

At the same time, U.S. District Court Judge Harold H. Greene found that, "Statistics show an imbalance in favor of white tenured employes, an overwhelming and unexplained concentration of black employes in Africa and an extremely small number of black employes in Latin America."

Despite being invited several times to submit data showing that these discrepancies "had a legitimate basis," Greene said, AID failed to "demonstrate in any way that racially neutral factors accounted for the gross statistical disparities, or even what those factors might have been."

Greene ruled in a suit brought by John H. Thomas, who is black and who was employed by AID in 1965 to serve in the agency's public health program in Vietnam. Thomas was hired on a "time-limited" basis, for 18 months, with the understanding that he could seek a tenured position.

Thomas worked for AID for nine years, but was never given tenure despite meeting all qualifications for tenure and statements from superiors in his performance evaluation rating lauding him. Thomas was separated from AID in 1974 when, purportedly for budgetary reasons, no position could be found for him.

In 1971, Thomas was transferred into job classifications from which tenure was not being granted."While in theory there could have been valid reasons for (Thomas') failure to achieve tenure or receive training opportunities and assignment to Latin America during his nine years at AID, the evidence adduced at trial demonstrates that these failures were the product of racial bias," Greene said.

Greene described AID's attitude concerning Thomas as "cavalier" and the efforts of his personnel officer on his behalf as "lethargic" and her testimony in court as indicating "her bias and lack of credibility."