A federal judge in New York yesterday barred the government from putting into effect anywhere in the United States its new rule requiring parental notification when teen-agers get contraceptives from federally funded clinics.

U.S. District Court Judge Henry F. Werker also ordered the Department of Health and Human Services to send notices to all its regional offices warning them not to put the new rule into effect.

The judge granted a temporary injunction Monday barring the department from putting the rule into effect, but it was unclear whether the order would extend beyond Werker's New York district.

Yesterday the judge cleared up any doubt, ruling that the temporary injunction applies to the HHS secretary personally, as the one responsible for promulgation of the rule. Werker said he would hold in contempt anyone who tried to put the rule into effect.

A Justice Department spokesman said the government would abide by the judge's ruling, while appealing the order as soon as possible. A hearing on whether to make the injunction permanent is scheduled for the first week of March. If, as expected by both sides, the judge issues a permanent injunction, the Justice Department is prepared to appeal on an expedited basis to the U.S. Court of Appeals for the Second District.

The new rule was scheduled to go into effect Feb. 25. It would affect between 4,000 and 5,000 federally funded family-planning clinics, requiring them to notify the parents of anyone aged 17 or younger who receives prescription contraceptives from the clinics.

One little-noticed provision of the new rule would change the way teen-agers pay for the contraceptives. Under current law, teen-agers can get them free or at reduced price if they can qualify as having a low income. Under the new rule, income of the teen-ager's family would be judged rather than the income of the teen-ager.

Judge Werker said in his Monday ruling that this would deter teen-agers from middle-income families from getting contraceptives at the clinics. They would cost more and parents probably would have to be contacted to determine the family income.

The ruling in New York came on two suits against the federal government--one from the State of New York and the state health department, represented by the state attorney general, and a second class-action group represented by the American Civil Liberties Union.

There are similar suits in at least three other jurisdictions.