Almost all the employees of the Wilson Center, a prominent nonpartisan foreign policy think tank in Washington, were placed on leave on Thursday and blocked from their work email accounts as Elon Musk’s task force quickly shut down most of the center.

About 130 employees received orders telling them not to return to the office after the end of the day, according to an email reviewed by The New York Times and people with direct knowledge of the actions.

The Wilson Center employees are to be paid while on leave but will be fired soon, in line with what has happened at other institutions that Mr. Musk’s workers have dismantled in recent weeks.

Only five employees will remain — a president, two federal employees and two researchers on fellowships. Those positions are mandated in the center’s congressional charter. The cuts align with an executive order President Trump signed in March.

Private donations to the center will be returned to the donors, according to a person familiar with the center who spoke on the condition of anonymity to avoid retribution. It was not clear what would be done with the center’s endowment.

On Thursday afternoon, dozens of employees carried boxes and bags filled with papers, plants and posters out of the center’s offices in the Ronald Reagan Building, which houses several government agency offices.

Tears glistened on the face of one woman as she departed. Workers wheeled out carts full of documents.

It was not clear on Thursday how the offices will be used, but the center’s charter requires the space to be part of the Woodrow Wilson Memorial.

On Monday, four members of the Musk team entered the center’s offices and began taking over its systems. The next day, the center’s president, Mark Green, resigned.

The Trump White House fired the center’s board members in recent weeks, one person briefed on the events said. Mr. Green, a former Republican congressman and ambassador, was told this week he would be fired if he did not resign, another person said. The White House declined to comment.

Mr. Musk’s government-overhauling workers have gutted several other institutions in Washington, including the United States Agency for International Development.

They have shut down centers that receive federal funding but that have done independent research for decades with the goal of giving nonideological expert assessments to policymakers, lawmakers and people outside government.

The Wilson Center, created in 1968 as a working memorial to honor the 28th president, Woodrow Wilson, receives about 30 percent of its funding from Congress; the rest comes from private donations.

The center has been run by former Democratic and Republican officials appointed by the board. Before Mr. Green, who led U.S.A.I.D. in the first Trump administration, became president and chief executive of the center in 2021, Jane Harman, a former Democratic congresswoman from California, ran the think tank.

The center has been a gathering place for scholars in all areas of foreign policy over the decades. It houses the personal library of George F. Kennan, the diplomat and policymaker who studied the Soviet Union. On Thursday, the director of the Wilson Center’s Kennan Institute, Michael Kimmage, posted photos of the library online and compared it to the library of ancient Alexandria, which “fell victim to political vicissitudes and war,” he wrote.

One question is what will happen to those materials and extensive digital archives that the Wilson Center has compiled. Researchers from around the world have used the archives for projects, and scholars especially value the center’s records of documents from the Cold War era.

A person familiar with the center said that it also housed historical records from Wilson’s campaign and presidency.

The center’s more than 50 fellows were expected to be paid until the end of their program, but those who are foreign citizens expect to have their visas canceled. Two of the fellows are at the center through a program for scholars whose work endangers them in their home countries, according to a person familiar with the center.

Each class of fellows is usually made up of academic researchers and one or more journalists working on book projects. Reporters from The New York Times have received fellowships.

A Trump administration official said that Natasha Jacome, a senior adviser to Mr. Green, was the center’s new president.