Health Education and Welfare Secretary Joseph A. Califano Jr. ordered an end to federal funding of most abortions for low-income women under the Medicaid program yesterday after federal Judge John J. Dooling in New York lifted a year-long injunction against the abortion ban.

The Senate, meanwhile, insisted by a 60-33 vote on adding substantial exceptions to the abortion ban as the price of continuing it for another year as a legislative provision of the money bill for the departments of Labor and Health Education and Welfare.

The original provision, first voted last year banned HEW from fundng abortions" except where the life of the mother would be endangered if the fetus were carried to term." It applied only to the year ending this Sept. 30, and had been held in abevance until yesterday by Dooling. The House on Tuesday voted 238-182 to continue if for another year without change.

The Senate earlier this year voted to provide exceptions to the ban and to abortion wherever a physician considered it "medically necessary" for what ever physical or psychological reason - an exemption which Sen. Pete V. Domenici (D-N.M.) said amounted to voting no ban at all.

Last night the Senate refused 59 to 34 to accept the more restrictive House language, then voted 60 to 33 to go back to conference with the House for further negotiations on a possible compromise between the positions of the two chambers.

In recent years, the federal government has been paying for about $250,000 to 300,000 abortions annually for low-income women under the medicaid program.

Dooling held up enforcement of the prohibition, but the Supreme Court, in effect, told him to lift his injunction and he did so yesterday. The high court ruled, in effect that the government can decline to pay for abortions even though they legal if the woman can pay them herself.

Califano order said that hence forth HEW will fund abortions under Medicaid only where the attending physician, on the basis of his or her professional judgement has certified that abortion is necessary if the life of the mother would be endangered if the fetus were carried to term." A department spokesman said the orders us effective immediately.

He said the department is not issuing any medical advisories and will leave it up to the physician to determine when and under what conditions he or she should certify an abortion to save a woman's life.

Califano also said the department will obey certain interpretive statements made by House-senate conferees on the bill last year which some what broaden the statutory life-of-the-mother exemption.

These statements, included in a report on last year's bill, declare that Congress intends to permit Medicaid abortions to terminate ectopic (fallopian tube) pregnancies and permit federal funds to be used for treatment of rape or incest victims and for drugs and devices to prevent implantation of the fertilized ovum on the uterus wall.

Califano said Medicaid funds will "continue to be available for such medical procedures." He added that treatment of rape or incest eligible for funding would be "prompt treatment before the fact of pregnancy is established." Department spokesmen said this meant use of a "morning after" pill or an intra-uterine device soon after intercourse or a dilation and curettage (scraping the uterus) within one or two weeks after intercourse, not an abortion many weeks afterward.

HEW spokesmen refused to estimate how many of the 250,000 to 300,000 abortions currently performed annually would become ineligible for Medicaid funding Califano's order. But opponents of the abortion ban have estimated that the large majority of such abortions do not fall under anu of the exemptions.

Califano's order applies only to the remainder of this fiscal year - through Sept. 30. If Congress ends up changing last year's language or conference advisery statement, Califano would have to revise his order to take these changes into account.