The protections are due to take effect two days before Donald Trump takes office.
Under the rule, states are legally required to distribute federal funds for services related to contraception, fertility, pregnancy, sexually transmitted infections and breast and cervical cancer screening — regardless of whether they also perform abortions.
A non-profit organisation, Planned Parenthood partly uses government grants to pay for contraceptives and health checks as well as cancer and STI screenings for low-earners in the US.
Federal rules already prevent the healthcare provider from spending any of the government funding – around $70m (£59m) – on abortions. Around half of the organisation's clinics do not perform the procedure.
Republicans in Congress have repeatedly threatened to cut off Planned Parenthood clinics and in September dozens of conservative states backed proposals to defund the service, prompting the Obama administration to introduce the proposals.
Mr Trump has previously praised Planned Parenthood, acknowledging that it “helps millions and millions of women” who go to it for health services such as breast cancer screening.
But he ran a staunchly pro-life campaign, saying it should be up to individual states to decide whether they should provide the service.
In March he said that if abortions were banned, women should face “some form of punishment”. He later retracted his comments after they provoked uproar.
Mr Trump has also repeatedly threatened to abolish Obamacare – the outgoing president’s reform intended to improve access to affordable healthcare – among other laws brought in under the Democrat.
But undoing the new rule on clinics providing abortions would prove particularly time-consuming, the Department of Health has said, making it less likely the law will be revoked.
“This rule will strengthen access to essential services like cancer screenings and contraception for some of the most vulnerable patients in this country,” said Karen A Scott, the department's chief medical officer.
She continued: “Public comments showed overwhelming support for finalizing the rule, which clarifies that all organisations able to provide these services should be eligible to compete for funds.”
Cecile Richards, president of the Planned Parenthood Federation of America welcomed the rule but said the "fight is not over".
"We are deeply concerned about the future of health care access in this country with extremists like Mike Pence and and Tom Price at the helm," she said in a statement.
“We will not back down, and we will continue to fight for our patients’ access to care"
Diane Black, a Tennessee Republican who sits on the Select Investigative Panel on Infant Lives, said the Obama administration “will not have the last word” on the law.
“We should not be surprised that his administration would lash out with this eleventh hour power grab on the way out the door, but I am certain this rule will not stand for long,” she said in a statement.
“Come next year, our pro-life majorities in Congress will be positioned to work with President-elect Trump and pro-life nominee for Secretary of Health and Human Services, Dr Tom Price, to not only roll back this latest overreach but also to enact new legal protections for these most vulnerable members of our society.”
Amid mounting concerns about whether the next US administration would limit access to birth control, there have also been reports of American women stocking up on long-term contraceptives.
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