The Department of Health and Human Services is still paying for about 1,000 Medicaid abortions a week for low-income women, despite a June 30 Supreme Court ruling upholding a congressional ban on such funding.

Sources said yesterday that statistics compiled by HHS, but not yet released, show that during the second quarter of 1980 the states submitted payment claims for at least 13,000 Medicaid abortions, an average of 1,000 a week, and that claims are still coming in at the same rate or higher.

HHS said yesterday that it intends to pay for these abortions, even though virtually all of them -- except a tiny handful involving pregnancies threatening the life of the woman or resulting from rape or incest -- are theoretically ineligible for federal funding under the Hyde amendment, which the Supreme Court upheld June 30.

HHS says it is continuing to pay for the abortions because technically the Supreme Court ruling is not yet final. The court has before it a petition from the American Civil Liberties Union for a rehearing, and until the court rejects that petition -- as most observers believe it soon will -- a January lower court order to continue the funding remains in effect.

HHS Secretary Patricia Roberts Harris has said that her department will pay for abortions performed under Medicaid until the Supreme Court ruling is made final and the lower court order vacated.

This situation -- continued funding of a wide range of abortions even though Congress has voted to cut the funding off and the Supreme Court has upheld the cutoff -- has so infuriated abortion foes that Rep. John Ashbrook (R-Ohio) pushed through the House this week an amendment ordering Harris to stop the funding immediately, even if the Supreme Court hasn't finalized its June 30 decision.

Before the amendment by Rep. Henry Hyde (R-Ill.) was adopted, the federal government was paying for about 295,000 Medicaid abortions a year. The Hyde amendment cut the federally paid total to 2,100 for fiscal 1978 and 3,900 for fiscal 1979.

However, a New York judge last January suspended the Hyde amendment and HHS started paying for abortions again, although the rate of state payment applications so far this year only seems to be about 50,000 a year. The low rate may merely reflect a paperwork delay in submitting bills.

Most observers believe that once Harris finally puts the Hyde amendment into effect, the federal payments will again be available for only 3,000 to 4,000 abortions a year.

There is considerable speculation, however, as to how many abortions the states will continue to pay for entirely out of their own funds, without federal reimbursement.

At present, according to the Alan Guttmacher Institute, nine states and the District of Columbia are voluntarily paying for a wide range of "medically necessary" abortions, a broad definition permitting far more abortions than the Hyde amendment.

These 10 jurisdictions paid for an estimated 72,000 abortions for low-income women in 1978, the last year for which figures are available. In addition to the District the nine states are: Maryland, Alaska, Colorado, Hawaii, Michigan, Oregon, North Carolina, Washington and New York, which paid for the most abortions -- 41,000.

Unless their legislatures change their laws, these states will probably continue to pay for 72,000 abortions a year or thereabouts. Abortion foes are expected to make concerted efforts, particularly in New York and Michigan, to alter the policy.

A dozen other states have restrictive abortion laws and regulations but at various times had been ordered by the courts, pending the Supreme Court's decision, to perform abortions for low-income women on a more liberal basis.

All told, these states paid for about 120,000 abortions in 1978. They include California which paid for the most abortions by far, 100,000, Connecticut, Georgia, Illinois, Louisiana, Minnesota, Missouri, New Jersey, Ohio, Pennsylvania, West Virginia and Wisconsin. Once the Supreme Court finalizes its June 30 decision, most of these states will be freed of court orders and and will cease paying for most abortions.

California and New Jersey, however, could be exceptions, because court battles against an abortion cutoff there focus on state constitutional provisions. Their supreme courts might conceivably rule that the state constitution requires continued abortion payments, even though federal support isn't available.

All the remaining states have restrictive policies or are in unclear legal status and aren't expected to pay for abortions themselves.

In sum: if the 10 "voluntary" jurisdictions continue their current policies, about 70,000 to 75,000 low-income women a year will get abortions paid for there without federal help. That will likely be the national total unless California and New Jersey are ordered by their courts to continue.