A divided U.S. appeals court panel in California yesterday reinstated the indictment of draft protester David Alan Wayte and upheld the legality of the draft registration program.

The decision reversed a District Court holding that government officials said they feared might have jeopardized the entire Selective Service registration system. Many federal prosecutors had been reluctant to proceed with further indictments.

The American Civil Liberties Union said it would appeal the 2-to-1 ruling to the full 9th U.S. Circuit Court of Appeals.

Wayte, a former Yale University philosophy student, argued that he was the victim of selective prosecution because of his public opposition to the registration. He also said the program had been put into effect in 1980 without a 30-day public comment period required by law. U.S. District Court Judge Terry J. Hatter Jr. shocked government officials on Nov. 15 by ruling in Wayte's favor.

Yesterday the panel said Wayte failed to show that the "government focused its investigation on him because of his protest activities." The court also said that the 30-day waiting period is only required when the government promulgates regulations, not proclamations such as President Carter's draft registration proclamation.