Selective Service Director Thomas Turnage acknowledged yesterday that an even higher percentage of young Americans have failed to register for the draft in recent months than in prior years.

But he defended the program in a House Judiciary subcommittee hearing against criticism that it is unwise and unenforceable.

Turnage, a retired Army major general, said only 87 percent of men born in 1964, and who become eligible for the draft this year, have registered.

"While this percentage is lower than the 93 percent attained in the earlier year groups, we are not alarmed since we know there will be a sizable number of tardy registrations in the coming months," he said.

Subcommittee Chairman Robert W. Kastenmeier (D-Wis.) cited the number of nonregistrants as an indication that the "credibility" of the draft registration system is open to question.

Turnage said the figure for nonregistrants "must not be taken as the number of violators" because only those who knowingly refuse to register have broken the law.

A General Accounting Office report released at the hearing said the number who have failed to sign up is about 700,000. Turnage said he could not explain the discrepancy.

"We presently have 8,365,000 registrants on hand from a potential registrant population of 9,039,000. Thus, there are approximately 674,000 nonregistrants," Turnage said.

Turnage said those who fail to register for the draft will start losing "the advantage of anonymity" in August, when the agency starts matching its registrant files with Social Security lists.

He said the names of 225 "probable violators" already have been turned over to the Justice Department for investigation or prosecution for failing to register.

Turnage also said he supports legislation that would deny federal aid to students who fail to register.

The subcommittee held hearings on the level of compliance with peacetime draft registration, which was resumed in July, 1980, with men born in 1960 and 1961.

David Landau, a lawyer for the American Civil Liberties Union, accused the administration of singling out conscientious objectors for prosecution.

"It is all too clear now that the first resisters to be prosecuted will be COs," Landau said.

"In the near future we are likely to witness the imprisonment of hundreds of young men for adhering to their religious and political beliefs," Landau said.

The Rev. Barry Lynn, president of Draft Action, a major antidraft group, said the Selective Service has repeatedly said registration would increase with indictments.

"This has not happened and is not likely to happen," he said. "The whole system, even on its own terms, doesn't work."