A sensitive new prenatal test could prevent 5,000 births a year of babies with grim spine and brain defects.

But it will not come into routine use for five years, say federal health officials, because -- in the words of one -- "it raises so many moral, ethical, legal, economic and medical questions, more even than heart transplants."

It is really a series of tests.

The first is a check of the blood for a substance called alpha-fetoprotein, or AFP.

AFP is a protein that every fetus produces. But when there is a defect of the developing baby's neural tube, its embryonic brain and spinal cord, there is more of it. A high level in the mother's blood -- usually in the 16th to 18th week of pregnancy -- may signal this and the possibility of spina bifida (open or incomplete spine) or anencephaly (lack of or incomplete brain).

If the first blood test is positive, it is followed by another. Then, if that, too, is positive, an ultra-sound "photo" of the fetus is made, and finally an amniocentesis, or tap of the amniotic fluid surrounding the baby.

AFP testing is already on the increase. Perhaps 50,000 women will take advantage of it this year.

But rushed into use, then misused or inexpertly used, the testing could cause as many human problems as it avoids.

The testing may occasionally produce a "false positive" reading, possibly inducing a parent to abort a normal child.

Like other prenatal tests, this one means that some parents who use it must decide whether to carry a probably deformed fetus to term, or abort it.

"Our association feels this test should be available," says Carol Buchholz of East Rockaway, N.Y., a mother of an afflicted youngster and an official of the Spina Befida Association. "But we also feel there should be understanding and help for those who choose to have their children."

Still, says Surgeon General Julius Richmond, this testing could play a major role in reducing infant death and disability and avoiding thousands of family tragedies.

"I feel very strongly about this," he said in an interview. "As a pediatrician, I've seen hundreds of families who had to face very severe difficulties."

This testing is already being done on 40 to 50 percent of all pregnant women in Great Britain, and the figure will probably near 100 percent in a year or two. Britain, with its government health system and calmer views on malpractice and abortion, has managed to avoid great problems.

Spina bifida and anencephaly occur in between one and two births per 1,000, about as often as the far better known Down's syndrome, or mongolism.

All anencephalic babies and some with opina bifida die quickly. Many affected children lead institutionalized or homebound lives because of their extensive physical and often mental crippling.

About 20 percent of spina befida children may be normal or virtually normal, however, with help, and others can be helped by surgery and education.

These facts were reported at a recent three-day conference here on AFP testing. The meeting was sponsored by the new National Center for Health Care Technology, as its first exercise in gathering doctors to consider valuable yet worrisome new methods so practitioners can decide what to do about them.

Dr. Seymour Perry, the center's director, and others described the problems:

Amniocentesis, the final confirmation, has been pronounced generally safe by U. S. officials. But British doctors think it may produce some ill effect in mother or baby in from 1 to 2.5 percent of cases.

From 1974 to 1978, three to five British AFP tests and follow-ups per 1,000, were "false positives." With such an indicator, the most common decision by percents would be to choose an abortion, which means a normal fetus would die. New methods could reduce the false positive results to one instance per 2,500 to 3,000.

Parents may sue if defective testing produces a false positive. Or they may sue if they have a defective child, and their doctor hadn't offered the tests.

An AFP test costs up to $35, amniocentesis up to $525, and a whole array of tests may cost nearly $800.

Nationally, routine testing could cost as much as $125 million. But a federal Center for Disease Control study says savings could be twice that, including $50 million a year otherwise needed for custodial care of disabled children.

The officials could be wrong when they say it will probably take about five years for this testing to become standard. It is already available in some major medical centers, especially if parents ask for it.

The Food and Drug Administration expects to propose regulations soon to permit sale of a medical test kit to doctors, under specific conditions.

"I think good facilities will come into being," Perry said. But both he and the surgeon general said they think this testing should be expanded step by step, with pilot programs to make sure it is done expertly and humanely.