The Reagan administration yesterday issued a regulation requiring the nation's 5,000 family planning clinics to send registered letters to parents to inform them when their daughters age 17 and under receive prescription birth control devices.

Civil liberties and family planning groups immediately filed suit against the regulation, which is due to take effect Feb. 25, and a federal judge in New York ordered the administration to show cause why the rule should be promulgated.

Fifty-eight health and religious organizations, ranging from the American Medical Association to the Salvation Army, also said in a statement yesterday that the new rule will not help teen-agers avoid pregnancy, and will not improve communications in families, but will "most assuredly threaten the health and welfare of thousands of young people."

The new rule is designed to "protect the health and safety of minor adolescents who are given prescription birth control drugs or devices paid for with taxpayer dollars," said outgoing Health and Human Services Secretary Richard S. Schweiker.

One of the chief reasons for establishing the rule was to assure that parents become involved in questions of health, sex, and pregnancy when their minor children get contraceptives from a clinic, HHS said in an explanation of the rule published in the Federal Register.

The rule requires that the clinics send a notice to parents within 10 days of the time children 17 or under receive prescription contraceptives, which include birth control pills, the diaphragm and the intrauterine device, or IUD.

Opponents predict that such a notification letter will scare off as many as a quarter of the more than 682,000 teen-agers who use federally funded birth-control clinics each year.

They say this, in turn, will add to the 474,000 pregnancies and abortions teen-agers underwent last year, possibly tens of thousands more.

HHS said it remained "unpersuaded" by these arguments, and said that there is no good data to support these conclusions. The document speculated that the opposite may be true--that notifying parents may get teen-agers to be more cautious about having sex and using contraception.

But the issues involved in what is called by opponents the "squeal rule" go far beyond law and health into the fields of morality and philosophy.

Both sides see this rule as a signal of a change in the direction of government policy.

"There is a signal here," said Anthony Robbins, director of the American Public Health Association, a group opposed to the new rule. "This is just the first of many efforts to destroy such things as the family planning program."

Proponents of the notification rule agree that this is only the beginning.

"I think it would be a logical extension of HHS policy to extend this kind of rule to to venereal disease and drug abuse. These are serious problems that a child shouldn't be left alone to face. I believe there will be a push for legislation in those areas as well," said Peter Gemma, executive director of the National Pro-Life Political Action Committee.

The $24 million family planning program gives "children an opportunity to experiment with sex and and drugs and so on, and not have to face their parents, not have to face the responsbility for doing it," he said.

"Free contraceptives and the idea of sex for kids has undermined the role of parents in disciplining and setting standards for kids," Gemma said. This regulation, he said, will make sure that parents do get involved when children get into trouble, and will make sure parents and children communicate about sex and contraception.

At a news conference yesterday sponsored by 58 health, religious, and political organizations, Faith Johnson, representing the United Church of Christ's Board for Homeland Ministries, described a strikingly different view of how the problem of teen-age sex and pregnancy should be handled.

She said her group finds it "hard to envision that a letter or phone call from a family-planning counselor informing parents that contraception has been provided will enhance family relationships."

Opponents of the rule say that children who have a good relationship with their parents will naturally discuss sex and contraception. Those who don't may be frightened away from clinics if they think the clinics will tell on them.

Many family planning clinics believe the confidentiality they offer teen-agers is crucial to their continued operation. They say that they live in the real world, the children already are having sex, many are not speaking to their parents about it, and what the clinics are doing is simply preventing pregancies.

In a question-and-answer session yesterday, Johnson said that if her daughter were afraid to talk to her about contraception, "I would want her to have the information anyway. I would want her to go to the clinic. Pregnancy is the issue."