The Federal Election Commission moved yesterday to assess a $5,000 civil penalty against the American Federation of State, County and Municipal Employes for the union's alleged failure to report its costs in preparing a 1976 political flyer aimed at defeating Gerald R. Ford.

The electoral regulatory agency said in a suit filed in U.S. District Court here that the union spent $983.73 to produce and distribute a caricature of Ford embracing former President Richard M. Nixon.

The flyer carried a quote from a speech given by then Vice-President Ford on July 25, 1974, saying, "I can say from the bottom of my heart - the president of the U.S. is innocent, and he is right" In addition, the cartoon likeness of Ford wore a "pardon me" button on his lapel.

The election commission said in its suit that the union violated federal election rules by not reporting the expenditure, although the union did report spending $23,858.14 to help President Carter get elected.

The election commission said it "has been unable through informal methods of conference, conciliation and persuasion" to reach an agreement with the union over the disputed flyer. The case will be heard by Judge John Lewis Smith.