Taxpayer-funded family planning clinics must stop referring women for abortions immediately, the Trump administration has announced, declaring it will begin enforcing a new regulation hailed by religious conservatives and denounced by medical organizations and women’s rights groups.

The head of a national umbrella group representing the clinics said the Republican administration is following “an ideological agenda” that could disrupt basic health care for many low-income women.

Ahead of a planned conference on Tuesday with the clinics, the Department of Health and Human Services formally notified them that it will begin enforcing the ban on abortion referrals, along with a requirement that clinics maintain separate finances from facilities that provide abortions.

Another requirement that both kinds of facilities cannot be under the same roof would take effect next year.

The rule is widely seen as a blow against Planned Parenthood, which provides taxpayer-funded family planning and basic healthcare to low-income women as well as abortions that must be paid for separately.

The organization is a mainstay of the federally funded family planning program.

Planned Parenthood’s president, Leana Wen, said in a statement that “our doors are still open” as her organization and other groups seek to overturn the regulations in federal court.

“We will not stop fighting for all those across the country in need of essential care,” Wen said.

HHS said no judicial orders currently prevent it from enforcing the rule while the litigation proceeds.

Clare Coleman, president of the umbrella group National Family Planning & Reproductive Health Association, said: “The administration’s actions show its intent is to further an ideological agenda.”

Abortion opponents welcomed the administration’s move on Monday.

“Ending the connection between abortion and family planning is a victory for commonsense healthcare,” Kristan Hawkins, president of Students for Life, said in a statement.

Known as Title X, the family planning program serves about 4 million women annually through independent clinics, many operated by Planned Parenthood affiliates, which serve about 40% of all clients. The program provides about $260m a year in grants to clinics.

The family planning rule is part of a series of Trump administration efforts to remake government policy on reproductive health.

Other regulations tangled up in court would allow employers to opt out of offering free birth control to female workers on the basis of religious or moral objections and grant healthcare professionals wider leeway to opt out of procedures that offend their religious or moral scruples.

The American Medical Association is among the professional groups opposed to the administration’s policy, saying it could affect low-income women’s access to basic medical care, including birth control, cancer screenings and testing and treatment for sexually transmitted diseases. By law, the family planning program does not pay for abortions.

The Trump administration’s policy echoes a Reagan-era regulation that barred clinics from even discussing abortion with women. It never went into effect as written, although the supreme court ruled it was appropriate.

The policy was rescinded under Bill Clinton.