The Federal Aviation Administration said yesterday that it will change its method of reporting near collisions in the air because "cracks" in the system had caused hundreds of reports from pilots not to appear in national statistics.

FAA Administrator Donald D. Engen said the agency is divided into nine regions, and regional reports of near collisions often fell into "little pockets" and never made it to Washington to be counted. Engen said the agency has taken "corrective actions" to centralize reporting by requiring that all raw report information on near collisions be forwarded directly to Washington.

Charles Hoch, manager of the FAA's safety analysis division, said 328 near collisions reported to regional officies during 1983 and 1984 never reached Washington to be included in national totals.

Engen announced that he will name an outside auditor to review the FAA reporting system.

The FAA came under fire earlier this year when Ralph Nader's Aviation Consumer Action Project charged that the FAA greatly underreported the number of near collisions in the air in the past two years.

Last January, the FAA reviewed regional office reports of near collisions to 1983, spokeman Dennis Feldman said.

The review uncovered 167 near collisions that went unreported in federal totals last year. The new incidents brought the 1984 total to 592.

In 1983 the FAA reported 286 near collisions. After this year's review that figure was raised to 478, according to Hoch.

"We will never throw out another report again," Engen said.

Statistics this year show that from Jan. 1 through May 30 there have been 242 reported near collisions, a 20 percent increase over the year-earlier figure. Seven actual collisions have occurred this year involving general aviation craft.

By the FAA's definition, a near collision occurs any time a pilot perceives his airborne plane to be in danger of colliding with another, regardless of distance.

Engen said he is considering limiting the near-collision category to incidents involving planes that come within a "500-foot bubble" of one another.

A spokesman said the FAA intends to use both systems throughout this year and statistics will be available on all incidents regardless of distances between planes.