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Shutdown May Prolong Grant Lawsuits and Reinstatements

OCT 07, 2025
Justice Department attorneys on multiple research-related cases are currently furloughed, as are grant administration staff.
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Science Policy Reporter, FYI FYI
An empty office at the Department of Justice headquarters.

An empty office at the Department of Justice headquarters.

DOJ

The government shutdown is slowing some court proceedings over research grant terminations. Justice Department attorneys moved to delay various court deadlines related to restoring grants to Harvard University and the University of California because government attorneys are generally prohibited from working during the shutdown. The judges have so far granted short-term extensions for those deadlines, which DOJ attorneys still may not be able to meet if the shutdown continues beyond this week.

Proceedings also appear to have stalled in several other cases related to grant terminations and indirect cost caps. For some, no appeal has been filed, while others await hearings.

In the Harvard case, the judge directed the Trump administration to reverse more than $2.6 billion in federal funding cuts in early September but left it to Harvard and the administration to jointly establish “implementation details” before issuing the final judgment. Following the shutdown, the judge extended the deadline for a status report to Oct. 10.

President Donald Trump said the administration would “immediately appeal” the decision against it in the Harvard case.

In the UC case, university researchers won a temporary restoration of grant funding, including two separate rounds of grant reinstatements from the National Science Foundation — one in June and one in August — and another ongoing tranche of reinstatements from the National Institutes of Health and the Department of Defense. The appellate court granted a stay in the administration’s appeal to overturn the temporary restoration of funds, while the district court extended the deadlines to restore all grants to Oct. 10 for NIH and to Oct. 17 for DOD.

On top of the furloughed attorneys, the ability of federal agencies to service grants — including restoring funds to those that courts have ordered reinstated — appears to be hampered. Agencies including NIH and NSF say in their shutdown plans that researchers may continue work on current awards but the agencies will not award any new grants. Like DOJ staff, most employees at science agencies are furloughed during a government shutdown and are not permitted to work, even voluntarily. NIH and NSF’s plans both indicate that staff may not be available to provide oversight or administrative support, even of existing grants, and one court filing from DOJ specifies that NIH’s grant office staff are furloughed.

A Harvard spokesperson said on Sept. 19 that the Department of Health and Human Services had returned $46 million in research funding to the university. This amounts to less than 2% of the total funding to be restored. FYI has reached out to Harvard for an update.

For the UC system, NIH had already restored 52 grants to researchers before the shutdown and planned to review nine remaining grants for potential reinstatement by Oct. 3, while DOD planned to reinstate all grants by Oct. 10.

Other cases

Several other research-related court cases are also ongoing, including two that seek to restore NIH and NSF grants across many different universities and other research organizations.

The NIH case, first filed in April by the American Public Health Association and others, has already seen an order to restore all the covered grants that was subsequently reversed by the Supreme Court, which found that challenges to grant terminations are outside the jurisdiction of the district court that originally overturned the terminations. The district judge has repeatedly canceled and rescheduled hearings to determine how to move forward.

Citing previous court decisions, including the Supreme Court order, the judge in the NSF case opted to temporarily keep the grant cuts in place because she did not have jurisdiction to hear challenges to the cuts. The rest of the case will proceed in the same court. (One of the plaintiffs, the American Association of Physics Teachers, is an AIP Member Society.)

The Court of Federal Claims, where the Supreme Court says plaintiffs must file suits related to grant terminations, states that all scheduled matters will proceed as scheduled until further notice during the shutdown.

The administration has not moved to stay proceedings in any of the lawsuits related to indirect cost caps, which NIH, NSF, DOD, and the Department of Energy all attempted to instate earlier this year. NIH and DOE are currently appealing orders to undo the 15% cap. NSF moved to dismiss its own appeal last week, and DOD has not appealed.

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