By Karina Tsui and Chris Boyette

(CNN) — A federal judge on Tuesday temporarily blocked part of the Trump administration’s pause on federal grants and loans, just hours before it was set to take effect, as a slew of advocacy groups, charities, foreign aid and public health programs warned of its potential to upend American lives on an unprecedented scale.

US District Judge Loren L. AliKhan’s stay temporarily blocked part of Trump’s plans, preventing the administration from pausing payments for open awards – those already granted by the federal government – through at least 5 p.m. ET Monday, February 3.

Reactions to the freeze included a flurry of lawsuits, statements of concern from recipients of federal funds and warnings about what may be to come.

What is the funding freeze?

Hundreds of programs touching all corners of the US were placed under review, according to a document released by the Office of Management and Budget.

The White House later issued a memo appearing to limit the scope of the federal freeze, saying it only encompasses types of programs that may run counter to Trump’s recent executive actions on immigration; foreign aid; climate and energy; gender identity; ending DEI initiatives and preventing federal funding for elective abortions.

Yet the planned freeze – which could later resume and trigger a potential showdown at the Supreme Court – has left many non-profit organizations and government agencies at local, state and federal levels in a state of flux.

What programs aren’t included in the freeze?

The initial order Monday said the pause would not affect Social Security, Medicare benefits, or “assistance provided directly to individuals.”

But as confusion swept through organizations that rely on federal grants and loans for their operations, the administration had to further clarify the order.

On Tuesday afternoon, the Office of Management and Budget issued a Q&A saying the following also would not see funding pauses: “mandatory programs like Medicaid and SNAP (food stamps)” – as well as “funds for small businesses, farmers, Pell grants, Head Start, rental assistance, and other similar programs.”

“This is not a blanket pause on federal assistance and grant programs from the Trump administration,” press secretary Karoline Leavitt said during her first White House briefing.

But the confusion appeared to have an effect: For several hours on Tuesday, state Medicaid agencies were unable to access federal funds for the health insurance program that covers more than 72 million low-income Americans. During the afternoon, states started regaining access to the funding system.

The National Association of Medicaid Directors confirmed Wednesday it had received word Medicaid would not be part of the federal funding freeze. “NAMD has been notified that Medicaid is exempt from the federal payment pause,” NAMD Executive Director Kate McEvoy said in a statement to CNN.

What are the impacts right now? Confusion reigns

• Meals on Wheels programs, which rely on federal grants and serve more than 2 million senior citizens annually, were unclear about whether they would be impacted. “We’re still dealing with a lot of conflicting information. In short, 37% of Meals on Wheels funding comes from the Older Americans Act, which is a grant on the freeze list,” Jenny Young, spokesperson for Meals on Wheels America, told CNN on Wednesday. “Right now, we’re battling conflicting information as the White House has said Meals on Wheels would not be impacted.”
• Universities across the country are scrambling to figure out how a funding freeze could affect their research programs, students and faculty. Researchers at Gallaudet University in Washington, DC, said they were told to stop work on grant-funded projects, according to The Associated Press on Tuesday. Scientists could miss deadlines to present and share their work if funding freezes go forward, said researcher Lorna Quandt, who has a grant application pending. The Association of Public and Land-Grant Universities on Tuesday called the administration’s move “unnecessary and damaging,” saying that a federal funding freeze would “sideline” American scientists.
• The National Science Foundation, which funds a wide range of scientific research through grants to universities and research institutions, has paused all of its grant review panels this week as it works to reconfigure its grant-making process in light of Trump’s executive order, it said Tuesday.
• “The United States has a unique government-to-government obligation to Tribal Nations,” said Native American Rights Fund Executive Director John Echohawk in a statement following Trump’s announcement. “Because of this unique relationship, Tribal Nations and Native people are especially and disproportionately affected by any federal actions like today’s funding freeze.” NARF Deputy Director Matthew Campbell said Wednesday that “despite the additional guidance, many Tribes and Tribal orgs are not able to access or draw down their federal funds. This has an immense impact and we are investigating the matter.”
• Atlanta is impacted by the funding freeze, from affordable housing to salaries and public safety, Mayor Andre Dickens said in a statement Tuesday before the district court’s pause. Partner agencies were unable to access portals essential to conducting business, such as paying rent and operational costs, he said.
• In Colorado, the state’s Community Health Network said a pause in federal funding could impact more than 857,000 Coloradans who rely on care. Community Health Centers had difficulty accessing the system used to access grant money Tuesday, spokesperson Grace Trautman said, but those who were able to make requests did receive their funds Wednesday.
• Gian-Carl Casa, president of the Connecticut Community Nonprofit Alliance, told the CT Mirror that taking away federal funding “will cut a hole in the already-frayed safety net, through which tens of thousands of people who depend on nonprofit programs here will fall. … To implement this kind of order without regard for the impact on living, breathing people is beyond comprehension.”
• Tommy Sheridan, deputy director of the National Head Start Association, which serves nearly 800,000 low-income children from birth to age 5 and their families, told CNN that some Head Start programs were unable to access Payment Management Services – the federal system used to draw grant money – which could have forced some to close their doors as early as Wednesday. While Head Start programs are now able to access their federal funding, the association believes the brief glitch is connected to the administration’s freeze order, Sheridan said.

Impacts facing overseas humanitarian aid

The uncertainty facing the freeze is not limited to within the US. Secretary of State Marco Rubio on Tuesday added more exemptions to humanitarian programs that would otherwise be cut by the freeze on almost all US-funded foreign assistance.

In a waiver obtained by CNN, Rubio agreed this week to keep spending on humanitarian programs that provided “life-saving medicine, medical services, food shelter and subsistence assistance,” leaving out programs that involve abortions, family planning and transgender surgeries.

The move has caused more confusion among the humanitarian community – many of whom are at risk of layoffs and program shutdowns from the initial directive. The groups say they have not been informed or received guidance on the waiver.

Though it has only been a few days, implications have already been catastrophic for those in Gaza and Ukraine, humanitarian officials told CNN. One predicted that if the suspension continued for two more weeks, thousands could die.

And the freeze, if continued, could cause a number of organizations doing humanitarian work to close permanently, as they are not receiving the funding to keep paying their employees.

Is the funding freeze legal?

The freeze of federal grants and loans is queuing up a Supreme Court showdown over the Constitution.

“There’s every reason to think that, unless this memo is quickly rescinded, the litigation it is going to provoke will get to the Supreme Court in one big hurry,” Steve Vladeck, CNN Supreme Court analyst and professor at Georgetown University Law Center, said Tuesday.

Some non-profit groups, including the National Council of Nonprofits, filed suit in federal court in Washington, DC, on Tuesday. That led to the federal judge’s temporary, partial block of the plans to freeze aid.

“From pausing research on cures for childhood cancer to halting food assistance, safety from domestic violence, and closing suicide hotlines, the impact of even a short pause in funding could be devastating and cost lives. This order could decimate thousands of organizations and leave neighbors without the services they need,” said Diane Yentel, CEO of the National Council of Nonprofits.

At least 22 states, including New York and California, in addition to Washington, DC, have also sued.

CNN’s Jennifer Hansler, Tami Luhby, Andy Rose and Tierney Sneed contributed to this report.

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