The Justice Department filed suit yesterday against a New Mexico commuter airline, claiming that it refused to hire a Turk and other noncitizen pilots in violation of a provision of the 1986 immigration law barring discrimination against aliens who intend to become citizens.

The charges against the company, Mesa Airlines of Farmington, are the first under the antidiscrimination provisions of the new immigration law, which established a special Justice Department unit, the Office of Special Counsel for Immigration-Related Unfair Employment Practices, to prosecute such cases.

The department filed one suit with the Executive Office of Immigration Review on behalf of the pilot, Zeki Yeni Komsu, a permanent resident alien who has applied for citizenship, and another suit alleging that Mesa Airlines had engaged in a pattern and practice of discrimination.

It charged that the company keeps two lists of applicants for pilot positions -- one of qualified applicants who are citizens and another of qualified applicants who are not citizens -- and does not hire from the noncitizen list if there are any qualified applicants in the citizen pool.

"That's basically correct," said Gary Risley, general counsel to Mesa. "The way I've read the statute, that's perfectly legitimate."

Risley said the company's view is "if we have a sufficient number of U.S. citizens who are fully qualified for a position, we have a preference for the U.S. citizen . . . . One reason is generally we know U.S. citizens will be in the country, we don't have any problems with their visas expiring and things like that."

Although the law makes it illegal to discriminate against individuals based on their national origin or citizenship status if they intend to become citizens, it provides an exception in a case where an employer gives preference to a citizen over an alien "if the two individuals are equally qualified."

However, Lawrence J. Siskind, the special counsel in charge of the discrimination office, said the background of that provision, inserted by Rep. Daniel E. Lungren (R-Calif.), indicated that it was intended to apply only to cases involving two equally qualified individuals.

Mesa Airlines, Siskind said, is engaging in "wholesale discrimination" prohibited by the law.