Transportation Secretary Samuel K. Skinner said he likely will shift direct control of aviation security and intelligence matters from the Federal Aviation Administration to his office, a major recommendation of the commission that investigated the terrorist bombing of Pan American Flight 103 in December 1988.

Skinner, in an interview, also said he probably will take the commission's recommendation a step further by moving Coast Guard and maritime intelligence and security directly into the Transportation Department.

Skinner said a comprehensive plan for enhancing airline security will be announced next month, some of it building on the Pan Am commission's recommendations. He said he and FAA Administrator James B. Busey plan to meet in early June to approve a final plan, now being developed by task forces within the FAA and the Transportation Department.

His comments are another indication that the government is taking seriously a report by the President's Commission on Aviation Security and Terrorism, issued May 15. Unlike many dust-gathering federal commission reports, the Pan Am commission apparently stung the government, particularly with its descriptions of an often lax and confused security system at one of the world's potential terrrorist hot spots, Frankfurt, West Germany. "I think it's fair to say we've taken the report very seriously," Skinner said.

The report was highly critical of the FAA, Pan Am and others involved in aviation security before and after the Dec. 21, 1988, bombing of the Pan Am Boeing 747 31,000 feet over Lockerbie, Scotland. Among the major recommendations that would affect Skinner directly was one urging creation of an assistant secretary of transportation for security and intelligence to oversee functions now handled within the FAA.

The commission said that placing security and intelligence directly under the government's highest transportation official would enhance its importance and "allow it to interract more easily with other high-level components within the intelligence and law-enforcement communities."

The report said that the CIA should delegate a senior officer to work within the new Transportation Department office.

"I am leaning toward accepting in some form, probably a form very close to what the report recommends, elevation of the national security intelligence issues up to the secretary's office," Skinner said. "That would be not only for the FAA but also for the Coast Guard as well as the maritime industry, and any of those things that have national security issues. . . . I think that's a very solid suggestion."

Busey now reports to Skinner and the aviation security and intelligence operations report to Busey.

Skinner and Busey have made it clear that they were not in charge when Pan Am 103 went down, and probably would have done things differently. Their distance from the decision-making process at the time apparently will make it easier for them to implement major changes.

The commission's description of Pan Am's security program at Frankfurt and London was particularly scathing, especially because the FAA found serious deficiencies for eight months after the Lockerbie crash that were slow to come to the attention of top federal officials. Only after Busey became aware of the problem and personally intervened with the top management of Pan Am did the situation improve.

"I guess the real travesty would have been if we'd lost an airplane during that period," Skinner said. "So I thank God that during this period after Pan Am 103 until we really tightened down on what was really intended to be a very tight system, we were very vulnerable."

Skinner said he and the commission visited Frankfurt separately after the last changes were made, and things are going well there now.

"We both came to the conclusion it was in pretty good shape," Skinner said. "But it took a long time to get there and I was not satisfied. . . . We just got to make sure it does not happen again."

Skinner sidestepped another major commission recommendation -- that the FAA suspend its multimillion-dollar program to put 150 thermal neutron analysis (TNA) machines in key airports -- on the grounds that the bomb-detection system is cumbersome and inadequate.

Skinner said no other technology does the same job. For now, TNA is the best process available, he said, but acknowledged "there's a mixed opinion." He said he will not make up his mind until he receives the results of ongoing scientific studies.