Tough new congressional restrictions have cut federally-funded abortions for low-income women by an estimated 99 percent, according to Department of Health, Education and Welfare figures.

HEW Secretary Joseph A. Califano Jr. told a House subcommittee yesterday that abortions for low-income women financed under the Medicaid program plummeted to 2,421 in the last 11 months of 1978 because of the funding restrictions. Before the limits went into effect, HEW estimated that the federal government funded about 250,000 such abortions a year.

Califano said that, except for the though limits sponsored by Rep. Henry J. Hyde (R-Ill.), the government probably would have paid for about 200,000 abortions under the Medicaid program in the 11-month period last year.

The figure of 2,421 federally financed abortions appears to undercut the arguments of some abortion foes that the federal restrictions were so loose they would barely cut back the total of such abortions.

The total was the first made public by HEW since the Hyde amendment was passed and is based on a newly installed reporting system covering the period from Feb. 14, 1978, to Dec. 31, 1978.

The Hyde amendment, as refined by a House-Senate conference, bans federal funding of "abortion on demand." It allows federal funding only if the life of the woman would be endangered by continuing the pregnancy, or she would suffer severe, long-lasting damage to her health, or in cases of rape or incest.

While the amendment was intended to cut off mot federally funded abortions, no one knew how it would work out in practice. Some critics maintained that even as written, it was too loose and that the provisions on rape and incest and physical health of the mother were loopholes and would invite abuse.

Califano said that 1,857 of the 2,421 federally funded abortions in the period reported involved the life of the mother, 385 involved physical health damage and 61 involved rape or incest. The rest were not broken down.

Califano, who supports the tough funding restrictions, told the House Labor-HEW Appropriations subcommittee that some states are using their own funds to finance abortions for low-income women in cases that do not meet the federal criteria.

It is not known how many such abortions are being financed by the states, but the number may be substantial, according to Barbara Lindheim of Planned Parenthood in New York.

She said about 18 jurisdictions, including the District of Columbia, are using their own money, either voluntarily or under court order, to continue abortions for low-income women, even when federal reimbursement is not available.

She said women in these states -- which include Michigan, Illinois, New York, California, New Jersey and Pennsylvania -- were estimated several years ago to have more than three-quarters of all Medicaid abortions.

Lindheim said it is not known how many abortions these state are now financing, but the number could be large. In some jurisdictions, a court order continuing the abortions may be more restrictive than the state's previous rule but less restrictive than the Hyde amendment.

HEW's abortions surveillance unit in Atlanta said figures on abortions financed soley by the states are not available.