Three of the nation's top auto makers - excluding Ford Motor Co. yesterday filed suit in Federal District Court in Michigan challenging a Federal Trade Commission investigation of the auto industry begun more than two years ago.

The suit, filed by General Motors Corp., Chrysler Corp. and two GM dealers, alleged that the investigation violates constitutional safeguards against illegal search and seizure and exceeds the commission's authority. The suit also contends that the subpoenas issued to the companies would generate burdensome paperwork costs.

Alfred F. Dougherty Jr., who oversees auto investigation as director of the FTC's Bureau of Competition, had no comment yesterday on the suit.

The FTC's current investigation of the economic structure of the auto industry is the first comprehensive study of the industry undertaken by the agency in more than 35 years. When the FTC announced the probe, it said the investigation would focus on the economic performance, practices and methods of competitions domestic and foreign - firms that manufacture and distribute cars.

On the basis of the information obtained in the probe, the FTC said it would determine whether there is reason to believe that any of the statutes it administers were being violated.

The suit filed yesterday alleges that the FTC is using "inquisitorial powers" to obtain information for an economic study without stating the specific scope or purpose of the study or charging the industry with any suspected violations.

The suit asks the court to declare unlawful and void the subpoenas issued to the companies in July.