In an email sent to certain employees and obtained by Fortune, USAID’s Acting Executive Secretary, Erica Carr, asked staff to shred and burn classified documents and personnel documents cleared from the agency’s headquarters.

She told staff to meet at USAID HQ from 9:30 a.m. on Tuesday for the daylong event.

“Shred as many documents first and reserve the burn bags for when the shredder becomes unavailable or needs a break,” Carr said in the email. “If you need to use the burn bags, do not overfill, and ensure the burn bag can be closed with staples at the top.”

She added that burn bags should be labeled with the words “SECRET” and “USAID/(B/IO)” in a dark marker.

Classified government documents are sometimes disposed of via “burn bags,” but some have raised concerns about the directive due to the precarious legal circumstances around the agency.

The State Democracy Defenders Fund, a nonprofit organization focused on democratic integrity and transparency, sent a letter to the United States Department of Justice urging it to stop the destruction of documents.

“We urge counsel for defendants [the DOJ] and USAID to take reasonable steps to immediately stop the destruction of documents and spoliation of evidence and instruct defendants and relevant governmental third parties to preserve evidence,” the letter, sent by the organization’s Legal Director, Tianna Mays and reviewed by Fortune, said.

The letter cited a recent order from Judge Theodore Chuang that required “specific orders or other decision documents, signed by the authorizing government official, that authorized” decisions relevant to the case, including decisions to place employees on administrative leave and to terminate personal service contractors.

A union representing USAID staff also told the BBC it was “alarmed” by the directive and warned that documents involved “may be relevant to ongoing litigation regarding the termination of USAID employees and the cessation of USAID grants.”

One former USAID worker, whose identity is known to Fortune, said documents may still be preserved electronically, adding that the loss of the Ronald Reagan Building, the USAID headquarters, meant there was limited space to safely store hard copies.

Organizations fighting the administration’s plan to shut down USAID filed an emergency motion on Tuesday afternoon to try and pause the destruction of documents.

“Defendants are, as this motion is being filed, destroying documents with potential pertinence to this litigation,” the emergency motion said.

Later on Tuesday, the parties followed up with a joint status report which said that the government “will not destroy additional documents stored in the USAID offices in the Ronald Reagan Building without affording notice to Plaintiffs and an opportunity to raise the issue with the Court.”

The U.S. State Department and USAID did not immediately respond to requests for comment from Fortune.

USAID shut-down

The U.S. Agency for International Development has been almost entirely dismantled since Donald Trump took office.

The president publicly took issue with the agency before he was sworn in. His chief cost-cutter, Elon Musk, also publicly attacked the aid agency, labeling it a “criminal organization.” Since then, the pair have closed the agency’s offices, placed most staff on admin leave, and cancelled thousands of international aid contracts.

On Monday, U.S. Secretary of State Marco Rubio said the government was officially canceling “83% of the programs at USAID.”

“In consultation with Congress, we intend for the remaining 18% of programs we are keeping (approximately 1000) to now be administered more effectively under the State Department. Thank you to DOGE and our hardworking staff who worked very long hours to achieve this overdue and historic reform,” he said in a post on X.

There are still ongoing legal cases scrutinizing how the shutdown of USAID was carried out.

On Monday, a U.S. district judge ruled that the “unlawful”’” suspension of USAID funding probably violated the Constitution and ordered the Trump administration to release nearly $2 billion in foreign aid that had been withheld from humanitarian organizations.

The decision prevented the administration from continuing to withhold aid payments, which have delayed food and medical supplies in struggling regions worldwide. However, the ruling does allow the administration to proceed with plans to cancel future aid contracts.