Planned Parenthood supporters rally for women's access to reproductive health care on "National Pink Out Day'' at Los Angeles City Hall in 2015. (Nick Ut/AP)

A federal judge Thursday challenged a Trump administration proposal to overhaul funding for family planning programs after three national reproductive rights groups and the American Civil Liberties Union sued to block the moves.

Planned Parenthood and the National Family Planning & Reproductive Health Association said new grant rules announced in February amounted to a radical shift that would jeopardize the health of millions of low-income patients by requiring providers to prioritize practices such as abstinence over sexual health services, such as contraception.

The update is part of a larger effort by the Department of Health and Human Services to emphasize conservative priorities in its programs. In May, officials announced a second major change to the $260 million federal Title X family planning grant process. The proposed rule would require a “bright line” of physical and financial separation between organizations that receive that funding and those that provide abortions or referrals to abortion clinics. Planned Parenthood and other women's health centers have said they could lose millions of dollars each year as a result.

The lawsuit before the federal court was filed shortly before the second set of updates was announced.

In court Thursday, the three national reproductive rights groups argued that the changes were so substantive that they should be struck down pending public notice and comment because they introduced new criteria for grant applicants worth 25 percent of the scores used to select winners.

Alicia M. Hunt, an attorney for HHS, urged a judge to reject that argument, saying whatever new factors or weighting was introduced by the department, final award decisions were entirely up to senior department officials and off-limits to court review.

That did not appear to sit well with U.S. District Judge Trevor N. McFadden of the District of Columbia.

“Is it your position that the [grant notice] could say anything it wanted, and it doesn’t matter because the DAS [deputy assistant secretary] has final say?” asked McFadden, a 2017 Trump appointee, drawing the answer "yes.”

“But now you’re adding an eighth factor, and it’s the most important factor,” McFadden said of the change, which states that applicants will be judged on four new priorities and “key issues” in addition to seven previous criteria set by federal regulations since 1971.

“Isn’t that a dramatic impact,” McFadden asked, if recipients who previously scored up to 100 might now be graded only at 75.

The new factor includes a stress on counseling focused on “avoiding sexual risk” and “returning to a sexually risk-free status,” terms used for sexual abstinence education and “fertility awareness,” or the rhythm method for natural family planning, without mentioning contraception.

Hunt said the change is "merely procedural and does not directly affect the outcome, because the final decision-maker has the authority."

"If I find this eighth factor is in conflict with the [regulation], does that mean you lose?" McFadden asked Hunt at one point, before asking how to ensure that funding would continue for the fiscal year ending Sept. 30 if the new grant changes were not implemented.

After the hearing, the groups that brought the lawsuit expressed optimism.

Clare Coleman, president and chief executive of the National Family Planning & Reproductive Health Association, said: “I think we had a great day. I think the judge knew the importance of Title X. … I feel confident he heard the arguments we were advancing.”

Ariana Eunjung Cha contributed to this report.

Read more:

Trump administration will pull funds from groups that perform abortions or provide referrals

Is it a gag rule after all? A closer look at changes to Title X funding regarding abortion.

‘Gifts from God:’ How ancient religions are coming to terms with modern fertility methods