A simmering dispute between the Department of Government Efficiency and an independent agency dedicated to promoting peace broke into an open standoff involving the police on Monday, as Elon Musk’s government cutters marched into the agency’s headquarters and evicted its officials.

The dramatic scene played out in Washington on Monday afternoon as Mr. Musk’s team was rebuffed from the U.S. Institute of Peace, an agency that President Trump has ordered dismantled, then entered it with law enforcement officers. Agency officials say that because the institute is a congressionally chartered nonprofit that is not part of the executive branch, Mr. Trump and Mr. Musk do not have the authority to gut its operations.

“DOGE just came into the building — they’re inside the building — they’re bringing the F.B.I. and brought a bunch of D.C. police,” Sophia Lin, a lawyer for the institute, said by telephone as she and other officials were being escorted out.

George Moose, who was fired as the institute’s acting president last week but is challenging his dismissal, accused Mr. Musk’s team of breaking in. “Our statute is very clear about the status of this building and this institute,” he told reporters. “So what has happened here today is an illegal takeover by elements of the executive branch of a private nonprofit corporation.”

The standoff quickly became one of the most visible points of resistance to Mr. Musk’s effort to fire federal workers and dismantle whole agencies. And it underscored Mr. Trump’s willingness to push the legal limits of his authority in his drive to reshape the federal government and put even entities that have traditionally been independent under his thumb.

A spokesman for Mr. Musk’s team directed an inquiry to the White House. An administration official blamed the institute for not complying with an executive order signed by Mr. Trump in February, which listed the institute as one of four governmental entities to be “eliminated to the maximum extent consistent with applicable law” and directed them to “reduce the performance” to the minimum required by law within 14 days.

The institute was created by Congress in 1984 and works to prevent and end conflict, deploying specialists to work with U.S. allies, training peace negotiators and diplomats and briefing Congress. Since the February executive order, its website was updated with additional references to the “cost-effective” nature of its work, a likely bid to win the favor of Mr. Musk’s team.

It did not work. Institute leaders and the Department of Government Efficiency had been butting heads since at least Friday afternoon, when the White House sent all but three of the institute’s board members an email telling them they had been terminated.

The remaining board members — Secretary of State Marco Rubio, Defense Secretary Pete Hegseth and Peter A. Garvin, the president of the National Defense University — later replaced Mr. Moose as acting president with Kenneth Jackson, a State Department official who was involved in the dismantling of the U.S. Agency for International Development.

Ms. Lin said the institute was preparing to sue the administration over the removal of the board. Officials at the institute have refused to recognize those terminations.

Department of Government Efficiency officials first tried to gain access to the agency’s headquarters, just off the National Mall, on Friday afternoon, but representatives for the institute turned them away.

Mr. Musk’s team showed up again around 7 p.m. on Friday, accompanied by two F.B.I. agents, and showed the institute a document signed by the remaining board members that removed the institute’s acting president. But they left after a lawyer for the institute told them it was an independent agency outside the executive branch, Gonzo Gallegos, an institute spokesman, said in a statement on Saturday.

Over the weekend, the F.B.I. threatened institute employees over the lack of access to the building, Ms. Lin said.

She also said that Jonathan Hornok, the new chief of the criminal division of the U.S. attorney’s office for the District of Columbia, called George Foote, another lawyer for the institute, on Sunday night and made requests on behalf of Mr. Rubio and Mr. Hegseth to gain access to the institute’s “books and records.” When the institute resisted, he threatened a criminal investigation, she said. A spokeswoman for the U.S. attorney’s office did not respond to requests for comment.

By Monday afternoon, signs newly posted to the doors of the building warned against trespassing and appeared to have been hastily created. One informed readers that the building was “closed until furthr notice.”

Musk representatives arrived on Monday afternoon in a black SUV with government plates and were escorted by what appeared to be private security who arrived in separate vehicles and were dressed in street clothing.

They tried one entrance, but could not seem to find a way inside and instead circled the building before getting back into the SUV.

After several minutes, two lawyers for the institute emerged from the building and approached the vehicle. What followed was a windowside negotiation: Mr. Musk’s representatives in the car, including a man who identified himself as Mr. Jackson, the State Department official and newly installed agency president, appeared to ask the lawyers to get in.

“I mean, I don’t know where you’re going to take us,” Ms. Lin said, declining.

“We don’t want to sit in here,” added Mr. Foote, the second lawyer for the institute, in a mellow, coaxing voice. “We can take a walk. We’ll take a walk, come on. It’s a nice day.”

Behind the car’s tinted windows, that offer appeared to be declined, and negotiations continued as rush hour traffic backed up behind the stalled vehicle and drivers laid on their horns. The parties appeared to agree to a hold a meeting over a video call.

Mr. Musk’s team did not get into the building until officers from Washington’s Metropolitan Police Department showed up, Ms. Lin said. Institute officials had called the police to report that Department of Government Efficiency members were trespassing, she said, but the police instead cleared institute leaders from the building.

A police spokesman, Tom Lynch, said that officers were called to the scene on a report of an unlawful entry and said the police left after the people who were seeking unlawful entry had left. He did not say who those people were or provide more information on what happened at the scene aside from the fact that no arrests had been made.

Two of the men, Nate Cavanaugh and Justin Aimonetti, a lawyer, were the same Musk officials who this month forced entry to the African Development Foundation, one of the government entities mentioned in the February executive order. They did not respond to shouted questions.

Late on Monday night, members of the Musk team, who are said to work around the clock, were still at the institute. Mr. Jackson could be seen working in the office of the president. They had dinner delivered: Sweetgreen and six pizzas.

Eric Lee and Kent Nishimura contributed reporting.