The District, which has some of the nation's highest rates of abortion, teen-age pregnancy and illegitimacy, is losing a private agency that has been the major conduit for federal funds to clinics providing low-cost family planning assistance.

The U.S. Department of Health and Human Services last week rejected a $700,000 funding request by the D.C. Interagency Council on Family Planning for this fiscal year. The decision will force the council to close, and it jeopardizes grants the council channels to three family planning agencies in the District, council officials said.

High-level HHS officials insisted, however, the $700,000 will be spent on family planning in the District and no lapse in service will occur when the council runs out of money Nov. 30.

But they said they are unsure whether Howard University, Providence Hospital and Planned Parenthood of Metropolitan Washington -- the three clinic sponsors funded by the council -- would continue to receive funds.

"In terms of need, the District is right up there over the rest of the country," said Joseph J. O'Hara, executive director of the council. "If you look at the number of adolescent pregnancies, live births to unwed mothers and infant mortality rates here, D.C. is twice as bad as the national average."

Nevertheless, he said, "at the end of the month we will be defunct."

In 1980, the most recent year for which statistics are available, 21 percent of births in the District were to adolescents, according to O'Hara. Fifty-eight percent of births in the city were out of wedlock, and more than 13,800 abortions were performed, he said. The District's infant mortality rate was 24.6 deaths per thousand live births, nearly twice the national average of 12.6 per thousand.

HHS officials last week said low-cost contraceptive devices and physical exams, family planning advice and community outreach programs previously sponsored by the council still will be available to an estimated 10,000 persons expected to use the services.

"There will be no lapse, even though we have yet to decide whether to fund the delegate agencies," said Linda Marston, the HHS director for the region that includes Washington. "We haven't decided whether the money will go to the agencies or not."

Some HHS officials indicated the department probably will replace the Interagency Council with another umbrella agency.

O'Hara disagreed that there wouldn't be a lapse. "Let's face it, if the federal money does not continue to come into the District, many of those local clinics will be forced to close their doors," he said.

Last year, about 9,500 persons received services paid for by $1 million the council distributed to Planned Parenthood, Howard and Providence Hospital.

O'Hara said a factor in the HHS decision was the council's suspension last month of Planned Parenthood from the council's funding. He said the suspension was prompted by Planned Parenthood's refusal to accept a funding change designed to serve more patients with a budget cut by the Reagan administration.

Instead of providing funds outright to the three agencies, the council began reimbursing them on a per patient basis. That change would have provided service to 50 percent more patients despite a 25 percent cut in money, he said.

Spokesmen for Planned Parenthood would not comment about the issue.

HHS regional health administrator William D. Lassek said in a letter to the council, in an apparent allusion to the suspension, that "the mere dropping and adding of delegate agencies is completely unacceptable to this office."

He also said the council's funding was denied because it "operates precipitously, rather than thoughtfully and with reflection."

"We wanted to expand our services, especially to minority and low-income people," O'Hara said in defense of the council's action. "A large proportion of the people Planned Parenthood was seeing were non-minority and not District residents--exactly the opposite direction we wanted to go in."

Howard University, which last year received $302,000 through the council for three clinics managed by its Center for Family Planning, is "in a state of flux" because of the HHS decision, said Elizabeth Vieth, the center's project director. "We don't know what's happening. . . . HHS's regional office hasn't told us how they're going to fund this agency. That's what we're worrying about now."

Howard's clinics treat about 40 patients daily and offer services that include pelvic examinations, Pap smears, pregnancy testing, counseling for women and diagnosis and treatment of sexually transmitted diseases. The clinics also offer a referral service to the hospital's prenatal, hypertension and sickle-cell units. Patients pay according to their incomes.

Officials of Providence Hospital could not be reached for comment.

Patricia G. Shannon, a D.C. National Bank vice president who heads the council's board of directors, said she was "flabbergasted" by the decision to cut off funding.

"We'll fight this all the way because we've done everything we were supposed to. We have proceeded in a professional manner," Shannon said.

Council officials have asked HHS Secretary Richard S. Schweiker to overturn the regional office's decision.