Likewise, this would account for the ''un-Japanese'' appearance of the Kabuki actors, courtesans and samurai portrayed in paintings and on silkscreens. The people in this highly stylized art are invariably shown with the elevated nose, the slight swelling at the center of the brow, the pointed chin and flat cheeks that set the Ainu apart from typical Japanese.

Dr. Brace, writing in a recent issue of The American Journal of Physical Anthropology, said, ''There is more than a little irony in this whole picture: where the Ainu, so looked down upon in the traditional Japanese conception of the social spectrum, have had a genetic effect on the ruling classes of Japan that would be completely unexpected for a conquered and despised people presumed to have been exterminated.''

The proposed revisions in Japanese genealogy were based on a study of 34 features of the skulls and teeth of more than 1,100 skeletons of Japanese, Ainu and other Asian ethnic groups. The samurai skeletons analyzed were from victims of the Battle of Kamakura in the summer of 1333. The skulls, Dr. Brace said, consistently bore a strong likeness to the Ainu-Jomon characteristics.

Historical accounts furnish a possible explanation how some descendants of the Ainu came to be the celebrated warriors.

Dr. Brace and his co-authors, M. L. Brace and W. R. Leonard, said that when the emperor in Kyoto wanted to subdue unruly inhabitants on the eastern frontier, the area around present-day Tokyo, generals usually recruited armies from the very residents meant to be controlled, the Ainu. This practice had gone on for nearly two centuries, and these recruited warriors became the revered samurai, sword-wielding knights in armor whose exploits led to six centuries of military rule in Japan. Theory Is Disputed

''Because of the course of history and the regional shifts of power that occurred as the feudal system emerged in medieval Japan,'' Dr. Brace wrote, ''the genetic characteristics derived from the Jomon-Ainu continuum came to constitute a significant part of the biological makeup of the dominant military class.''

But Hisashi Suzuki, a retired professor of anthropology at the University of Tokyo, has denied that the fallen samurai of Kamakura, and thus succeeding generations of ruling classes, could be Ainu. Dr. Suzuki, reflecting the established view of Japanese anthropology, said that, despite some Ainu traits, the samurai physical characteristics were merely a local variant of modern Japanese features.