A federal judge in New York yesterday barred the government from putting into effect a rule that would require family planning clinics to notify parents when their children have received contraceptives.

U.S. District Court Judge Henry F. Werker granted a preliminary injunction against the rule, saying it would lead to an increase in teen-age pregnancy.

"The parental notice requirement is invalid because it contradicts and subverts the intent of Congress," Werker said in his ruling. "The court finds that the regulations constitute a blatant disregard for one of the main purposes" of the family planning law as passed by Congress.

Health and Human Services Department officials had no comment yesterday, but the American Civil Liberties Union, which brought suit on behalf of the state of New York and the New York health department, said the ruling probably will block implementation of the regulation nationally.

The rule requiring notification of parents was scheduled to go into effect Feb. 25. It would have required some 5,000 family-planning clinics that receive federal funds to mail a notice to parents within 10 days of prescribing a contraceptive to anyone 17 or younger. The three contraceptives included in the rule are the pill, the diaphragm and the intrauterine device.

The notification rule has been opposed by numerous health and civil liberties groups. It has generated more mail than any other proposed regulation in the department's history. Reagan administration supporters, however, say parents have a right to know what their children are doing, and the government should not be providing contraceptives to their children secretly without the parents' knowledge.

Werker said in 20-page opinion that it was unnecessary to consider deep constitutional questions on the matter, since the law itself and the documents surrounding it made clear that Congress never intended to make parental notification mandatory.

He also called one HHS argument "fatuous" and another "nothing more than an exercise in mere sophistry" when the agency claimed that it was not mandating family participation in contraception with this rule, but only facilitating it.

At the same time the ruling came in New York, other suits trying to stop the regulation had reached various stages in courts in Tennessee, West Virginia and the District of Columbia.

In arguments before U.S. District Court Judge Thomas A. Flannery in the District of Columbia, John Nields, an attorney for family planning groups seeking to throw out the new rule, said the regulation "blatantly contravenes" the law and would cause 33,000 teen-agers nationwide to become pregnant.

Nields said HHS bowed to "political pressure" from opponents of family planning in proposing the regulation.

But Theodore C. Hirt, an attorney for the government, told Flannery that the regulation was a "reasonable method" of implementing the law and that the government did not believe "there will be these dire consequences" of increased pregnancies as a result of the notification requirement.

"Parents have an interest in knowing what medications their minor children are taking," Hirt argued, saying that interest "could not be overlooked."

In response to a question by Flannery, Hirt said that before the rule was implemented 40 states had registered objections to it and no state had told HHS that it favored the rule.