The Federal Aviation Administration's special inspection of the nation's 327 airlines last spring found that, while 95 percent followed U.S. safety rules, the rest had problems and the FAA must improve surveillance of the industry.

The report of the 90-day inspection was released yesterday and comes amid renewed concern that the FAA is not equipped to keep pace with an industry changing rapidly since deregulation in 1978.

Some of the most serious problems among the 29 types of deficiencies found by the inspectors were that:

* Some airlines loaded and balanced planes unevenly, making them unstable in flight.

* Some flight crews did not record mechanical difficulties in their logs, meaning that a subsequent crew was unaware of them before takeoff and that mechanics did not know they needed to be fixed.

* Some crews were unfamiliar with the "minimum equipment list," an FAA compilation of all gadgets that must work properly before a flight is legal.

* Some mechanics were not properly trained to inspect planes for possible defects.

Deregulation has spawned many new airlines and new operating methods by veteran carriers and has given tremendous impetus to commuter airlines. These now provide the only scheduled flights to hundreds of small- and medium-sized communities.

The inspectors found that, "in those cases where there was an indication of a compliance problem," airlines involved were undergoing rapid expansion, contracting out many normal airline functions such as training and maintenance and experiencing financial difficulty or labor-management problems or both.

If those are characteristic of an airline's operation, the report said, that fact should trigger "increased FAA surveillance and increased efforts on the part of the air carrier to monitor compliance."

Since deregulation, rapid route expansion by some airlines has been accompanied by a financial recession that saw the industry suffer its worst losses, major retrenchment in wages and several bankruptcies. These included such big names as Braniff, Continental and Air Florida, the last of which prospered in the early days of deregulation but overreached and perished.

Transportation Secretary Elizabeth Hanford Dole ordered what she called the "white-gloves" inspection after several disquieting incidents, most prominently the deaths of 10 persons in the crash near Carbondale, Ill., of an Air Illinois flight in October 1983. Investigators found that the expanding commuter airline had received casual FAA surveillance. Air Illinois is no longer operating. After its initial sweep, the FAA gave follow-up inspections to 42 airlines, 16 of which incurred disciplinary or administrative actions. The biggest names on that list are People Express,, Alaska and Northeastern.

The major People Express deficiency was described by FAA and People Express spokesmen as a record-keeping error indicating that 55 pilots had not received required training. All were sent back to school briefly because that was the quickest way to solve the problem.

Cited discrepancies have been corrected on airlines still flying, FAA Administrator Donald D. Engen said in an interview yesterday. One of those, American Central, was grounded by the FAA last Saturday for continued violations after follow-up inspections.

Engen said FAA inspectors have become much more aggressive as a result of what was learned. "A lot of water has gone over the dam since Air Illinois," he said. "We grounded or curtailed operations of 15 airlines in 1984, more than we've ever done before. I think that's indicative of the strong attitude we're taking."

He agreed that the report said as much about FAA weaknesses as about those of the airlines.

"We learned that we were inconsistent in our enforcement and application of policies" from region to region and that "there was an increased use of contracting-out by airlines for maintenance, training and operational support," he said. Engen said FAA officials have stressed in recent meetings with airline representatives that a contracting airline retains responsibility.

One airline that passed inspection was Provincetown-Boston, later grounded by the FAA for 15 days after a tipster told inspectors that records had been altered. "We cannot afford to have falsifications," Engen said, adding that the FAA will move harshly against them.

The FAA is pursuing civil-enforcement actions against several airlines for violations of safety regulations discovered during the inspection, the report said.