Science 86, a Washington-based publication of the American Association for the Advancement of Science, yesterday won its third prize in five years in the prestigious National Magazine Awards.

The prize, for a Science 85 issue, was one of 13 announced during a luncheon at New York's Waldorf-Astoria Hotel.

Science 86, which publishes 10 times a year and changes its name with the advent of each year, was chosen out of a field of 59 entries for the American Society of Magazine Editors' "public interest" award. It honored a four-article package published last December on minimizing the risk of accidental nuclear war, called "Technology for Peace: Can Science Help Us Out of the Nuclear Nightmare?"

Robert E. Kenyon Jr., the head of the ASME competition, said the "public interest" prize is for articles that "produced clearly demonstrable results, such as legislation, investigation, letters to the editor and so on."

Allen L. Hammond, Science 86 editor, said the issue was "timed to build on the Geneva summit conference."

A magazine spokesman described the package as a report on the sophisticated technologies the United States uses to monitor Soviet weaponry, the political components of verification and the scientists who perform on-site nuclear power reactor inspections worldwide to discourage diversion of nuclear materials from peaceful purposes.

Perhaps the biggest single winner yesterday was Time Inc., which won three awards: for general excellence in a magazine with more than 1 million subscribers, to Money; general excellence in a magazine with a circulation of 400,000 to 1 million, to Discover, a scientific journal; and for design, for the redesign of Time itself.

The main reporting prize, "for the advancement of knowledge, enterprise, thoroughness and style of writing," went to Rolling Stone for extensive coverage on AIDS.

Other awards: for general excellence in a magazine with circulation under 100,000, to New England Monthly; for general excellence in a magazine with circulation 100,000 to 400,000, to 3-2-1 Contact, a publication for children; for "personal service," Farm Journal; for "special interests," Popular Mechanics; for photography, Vogue; for fiction, The Georgia Review; for essays and criticism, The Sciences; and for a single topic issue, IEEE Spectrum, for an issue on AT&T.