A small museum dedicated to the nation’s environmental history is now history, too.

On Monday, Lee Zeldin, the administrator of the Environmental Protection Agency, said he had shuttered the museum, which was inside the agency’s headquarters on Pennsylvania Avenue in Washington.

In a statement, Mr. Zeldin said the move would save taxpayers about $600,000 annually. “Our commitment to responsible stewardship of taxpayer dollars remains unwavering as I continue to oversee a line-by-line review of agency spending,” he said.

Created in 2016, the museum originally occupied a corner of the Ronald Reagan International Trade Building. In May, a $4 million expanded National Environmental Museum and Education Center opened inside E.P.A. headquarters.

Mr. Zeldin described it as a “one-room, little-trafficked museum” that is frequented mostly by agency staff members.

He also noted that it included exhibits about environmental issues faced by poor and minority communities, issues the Trump administration has said should not receive special attention. He called those displays a “political agenda” of the Biden administration.

“Gone are the days of funding partisan pet projects at the detriment of the American taxpayers and the agency’s mission of protecting human health and the environment,” Mr. Zeldin said.

He included an accounting of the museum’s annual costs: $123,000 for cleaning and landscaping, $207,000 for security guards, $54,000 for magnetometer and X-ray maintenance, about $54,000 for artifact storage and about $40,000 for maintenance of audiovisual equipment.

The closure comes amid complaints by President Trump that the Smithsonian museums have “come under the influence of a divisive, race-centered ideology” and that they promote “narratives that portray American and Western values as inherently harmful and oppressive.”

Former E.P.A. officials criticized Mr. Zeldin for closing the museum and said many of his reasons were faulty.

For example, Mr. Zeldin said the museum “conveniently omits any environmental progress” made during President Trump’s first term.

While Mr. Trump rolled back more than 100 air and water protections during his first term, the museum does mention his signing of a 2020 law that eliminated hydrofluorocarbons, a greenhouse gas. In smaller letters below, it notes that President Joseph R. Biden Jr. had designated a task force to promote climate change in federal agencies.

The museum included exhibits on all the previous E.P.A. administrators, including two from Mr. Trump’s first term, Scott Pruitt and Andrew Wheeler.

The museum did include a number of exhibits focused on environmental justice and efforts to address climate change, both of which were priorities of Mr. Biden’s. But those displays were designed in a way that allowed panels to be removed if, for example, an administrator wanted to focus on different issues.

“Oh for heaven’s sake,” Stan Meiburg, who served as acting deputy E.P.A. administrator from 2014 until 2017, said when he heard about the decision to close the museum. “I doubt very much this is about cost savings,” Mr. Meiburg said. “It’s about trying to erase the past.”