President Reagan's new antiabortion regulations for federally funded family planning clinics were denounced yesterday by the American Medical Association and challenged in federal courts by family planning groups and state governments.

AMA spokesman Harry S. Jonas told reporters that the group is concerned the Department of Health and Human Services, which published the final regulations in the Federal Register yesterday, "has exceeded its statutory authority in this matter and that the final regulations will have the effect of interfering with the physician-patient relationship."

Federally funded family planning clinics already are forbidden by law to perform abortions or to advocate or oppose abortion directly. The regulations also would forbid them to advise a woman, even in an indirect fashion, that keeping a baby, putting it out for adoption and abortion are all legal options for handling a pregnancy. In addition, a clinic would be forbidden to refer a woman directly to an outside medical facility providing abortions, even if she asked for one. A clinic that failed to obey the rules would lose its federal funding.

Under the regulations, if a woman asked for advice about a pregnancy, the federally funded clinic would be forbidden to list her options or to advise her what to do, according to HHS deputy assistant secretary for population planning Nabers Cabiness. Instead, the clinic would give her a list of outside prenatal and social service clinics that could include some clinics providing abortion services. Cabiness and other administration representatives said the regulations seek to limit the federally funded clinics, which serve more than 4 million women a year, to providing prepregnancy services such as contraceptive and fertility advice.

In separate lawsuits filed yesterday in Colorado, Massachusetts and New York, the Planned Parenthood Federation of America, National Family Planning and Reproductive Health Association and several state governments including New York and Massachusetts argued that the regulations reverse congressional intent as to how the law should be interpreted and are in some respects unconstitutional.

They said the regulations change interpretations of the law that Congress has accepted for 17 years allowing the clinics to list all medical options, including abortion. They also charged that the regulations cut off doctors' right and obligation to advise women of all their medical options, impinge on the woman's right to decide whether to bear a child, and, in a variety of ways, curb the right of organizations to use their own separate funds to advocate abortion outside the federally funded program.

Jonas and representatives of other medical groups charged that the regulations would forbid a doctor at a federally funded clinic to inform a woman that abortion is a lawful medical option not only in normal pregnancies but also in cases where the pregnancy is life-threatening. They said this would breach the ethical and legal requirements generally applicable to the practice of medicine.

Under the regulations, if a pregnancy had medical complications, the woman would be told to go to an outside facility for emergency medical services.