William H. Hudnut III, the Republican mayor of Indianapolis, yesterday said an effort by the Justice Department to scale back major affirmative action directives "is a political mistake as well as being morally and legally wrong."

Hudnut said he had written a letter to President Reagan complaining about the efforts because he thought the president "hasn't been briefed well on the issue by the people in the injustice department."

The letter said efforts to modify or eliminate a 20-year-old presidential executive order requiring affirmative action in hiring represents "an unfortunate step backward" and would turn "the clock far back on civil rights advances."

These efforts are supported by Attorney General Edwin Meese III and William Bradford Reynolds, the department's civil rights chief. The department has attempted to halt the use of racial hiring goals, supported by Hudnut, in an affirmative action case involving the Indianapolis police and fire departments.

Such action "sends the wrong message politically" to minorities and could damage the Republican Party, Hudnut told a news conference at the annual winter meeting of the U.S. Conference of Mayors.

Two other mayors, Donna Owens (R) of Toledo, Ohio, and Thirman L. Milner (D) of Hartford, Conn., appeared with Hudnut at the news conference and endorsed his stand.

"We haven't reached that goal in the country where we can say, 'Hallelujah. There is no discrimination,' " said Owens.