Rep. Charles E. Schumer (D-N.Y.) has asked the Justice Department to investigate the nation's largest private aviation organization for failing to register as a lobby and maintaining questionable ties to two former Federal Aviation Administration (FAA) chiefs.

In a formal request to the Justice Department's criminal division, Schumer said the Aircraft Owners and Pilots Association (AOPA), which represents 260,000 private pilots, has not filed lobbying reports with the House since 1979 and appears to "have flouted laws regulating lobbying activity."

"For the issues they're interested in, I have seen few organizations that have such dominance," Schumer said.

"If you look at the statistics, in terms of delays and safety, there seems to be an undue lean by the Federal Aviation Administration toward general aviation," Schumer added.

AOPA spokesman Edmund Pinto said the group spent only $4,000 on lobbying in 1979 and that its lawyers advised the AOPA that it need not register.

"You hire lawyers to advise you. That was their advice," Pinto said. He added that, within the last six or seven weeks, the group has looked again at its lobbying and decided to report its activities. AOPA officials said their group spends less than one percent of its annual $20 million budget on lobbying.

Under the 1946 Federal Regulation of Lobbying Act, every lobbying organization is required to register quarterly and disclose the source of its money and where it is being spent, even if the bulk of the group's activity is nonlegislative. Failure to comply is punishable by fines, a prison term and a three-year ban on lobbying Congress.

AOPA President John L. Baker said it is "unfortunate that the congressman went off half-cocked." He said he spoke with Schumer yesterday to arrange a meeting next week.

Schumer said he is concerned because the AOPA hired former FAA chief Donald D. Engen to head its Air Safety Foundation and works with another former FAA chief, J. Lynn Helms.

Helms is not on the group's payroll, Pinto said yesterday, and is involved in a project that includes four other aviation groups. Engen said he is involved in flight training and safety programs, not legislative activity.

Private planes have drawn attention in recent months after involvement in several near-collisions. Government statistics show that the majority of reported near-collisions involve at least one small plane flying under "visual flight rules," meaning the pilot is not being directed by air traffic controllers.

In August, a private-plane pilot who said he had lost a contact lense and was trying to find it, nearly collided with President Reagan's helicopter near the president's Santa Barbara, Calif., ranch.

Then, after an American Airlines jet and a small plane nearly collided over Los Angeles Aug. 11, FAA chief T. Allan McArtor issued an emergency order placing further restrictions on private planes flying around Los Angeles International Airport.

The AOPA joined a suit against the FAA and inundated members of Congress with an estimated 50,000 postcards and letters to protest the changes.

"We ought to be influential," Baker said. "We make a hell of an effort. We represent a significant cross-section. We're very good at what we do."

Baker said the private pilots' concern in Los Angeles was not access but safety and, after meeting with the private pilots, the FAA is working out a plan to establish new access paths for small planes around the airport.

"We deal in aviation safety, and that's hardly compatible with 'undue influence,' " FAA spokesman Bob Buckhorn said.

Buckhorn added that the agency encourages "input from all the users of the system, and that includes general aviation. But the final decision is the FAA's."