Dr. James B. Wyngaarden, new director of the National Institutes of Health, declared yesterday that he favors "freedom of choice" on abortion availability, a position that differs dramatically from the anti-abortion sentiments of President Reagan and other top health officials.

In his first meeting with reporters, Wyngaarden said he thinks abortion is a "personal" matter that should be "up to the individual" rather than regulated by the government.

Reagan wrote last month to conservative Sen. Jesse Helms (R-N.C.) to support passage of legislation this year to "restore protection of the law to children before birth." But Wyngaarden, 57, who heads the government's biomedical research program, said he takes a "more lenient point of view" of the need for such legislation.

Although NIH is not directly involved in providing abortions, Wyngaarden said the government program does support studies of prenatal diagnosis of fetal abnormalities that provide a "scientific" basis to help couples make decisions.

On a related issue of concern to some anti-abortion advocates, Wyngaarden also spoke in favor of considering federal funding of test-tube baby research in humans. He called it a "legitimate" area of study that could further benefit infertile couples.

While NIH supports animal experiments in this area, Department of Health and Human Services Secretary Richard S. Schweiker has not acted on a proposal to lift a ban on human fetal research. Neither did his two predecessors.

Wyngaarden's comments on abortion did not go unnoticed by his boss. Later in the day, Schweiker issued a statement saying, "Dr. Wyngaarden has told me that he was responding to a reporter's question about his personal belief, which differs from mine, and he has assured me he intends to fully support the president's position on this matter as well as all other administration positions.

"He has also told me that his personal views on this issue will not influence his performance as director of NIH," added Schweiker, a longtime opponent of abortion.

Views similar to Schweiker's have been voiced by Assistant Secretary for Health Edward N. Brandt Jr. and Surgeon General C. Everett Koop, a former activist in the anti-abortion movement.

Wyngaarden, a highly respected researcher, was sworn in April 30 as the 12th NIH director, a post vacated last summer by Dr. Donald Fredrickson. Wyngaarden gave up the chairmanship of the department of medicine at Duke University School of Medicine to take the NIH post.

He said yesterday that he had not been given assurances when he took the job that it would be isolated from politics but that he considered the position, by tradition, to be "very much of an apolitical nature."

Although Wyngaarden was a registered Democrat in North Carolina, he said that was not an issue when he was hired because he had not been active in politics.

Although he demonstrated his independence on topics such as abortion and test-tube babies, he emphasized yesterday that his new duties will be focused largely on stabilizing basic medical research in an era of declining funds.

Inflation has hit NIH's $3.6 billion budget in recent years, decreasing the number of grants that can be funded and the amount of money for training new researchers.

Wyngaarden said he also hoped to fund more clinical trials, in which researchers compare various modes of treatment on a scientific basis.

In addition to budget considerations, he must replace heads of several key institutes who resigned during the last year.