One Side of a Nuclear Waste Fight: Trump. The Other: His Administration.

Before the 2018 midterm elections, Senator Dean Heller stood with President Trump in the glittering Trump International Hotel near the Las Vegas Strip, looking out from the top floor, and pointed.

“I said, ‘See those railroad tracks?’” Mr. Heller, a Nevada Republican who lost his seat later that year, recalled in an interview. Nuclear waste to be carted to Yucca Mountain for permanent storage would have to travel along the tracks, within a half-mile of the hotel, Mr. Heller said.

“I think he calculated pretty quickly what that meant,” Mr. Heller said. “I think it all made sense. There was a moment of reflection, of, ‘Oh, OK.’”

Whether the waste would have traveled along those particular tracks is a subject of debate. But the conversation appears to have helped focus Mr. Trump, who in recent weeks seemed to end his administration’s support for moving nuclear waste to Yucca Mountain, a proposal that had been embraced by his appointees for three years despite his own lack of interest.

“Why should you have nuclear waste in your backyard?” Mr. Trump asked the crowd at a rally in Las Vegas on Friday, to applause, noting that his recently released budget proposal did not include funding to license the site, as previous ones had.

The story of the muddled and shifting position on Yucca Mountain is partly one of an administration focused on Mr. Trump’s re-election chances in a battleground state that he lost to Hillary Clinton by two percentage points in 2016. But it is also emblematic of a White House where the president has strong impulses on only a narrow set of issues, and policy is sometimes made in his name regardless of whether he approves of it.

In Mr. Trump’s decentralized administration, top aides and agency leaders have sometimes pursued their own agendas, at times creating politically perilous situations for him. The confusion around policy over the last three years has ranged from issues like the repeal of the program for undocumented immigrants known as DACA, largely steered by the attorney general at the time, to a more recent internal debate about a ban on some e-cigarette flavors, driven by the health and human services secretary.

The president made his latest move after a monthslong policy debate inside the White House over finally breaking with support for Yucca, officials said.

“While Congress has played political games over Yucca Mountain for years and failed to find a solution, the president is showing real leadership by respecting the people of Nevada and their wishes,” said Judd Deere, a White House spokesman. “President Trump is committed to finding the best options for the safe and efficient disposal of our nuclear waste.”

This article is based on interviews with nearly a dozen people familiar with the administration’s knotty relationship with the proposal.

Yucca Mountain, in the desert about 100 miles northwest of Las Vegas, was conceived as a permanent storage place for the nation’s radioactive waste, which is currently scattered across dozens of holding sites around the country.

Nationally, Republicans have long favored the proposal, which was developed in the late 1980s and signed into law by President George W. Bush in 2002. But Nevada politicians of both parties have remained steadfastly opposed to the policy, which is deeply unpopular in the state.

“I don’t know of a major elected official in Nevada today, or in the last five years or 10 years, for that matter, that hasn’t specifically pushed to keep the waste out of the state,” Mr. Heller said.

The project was halted by President Barack Obama, partly at the urging of Harry Reid, a Democrat from Nevada who was the Senate majority leader at the time, but most Republican leaders outside of the state remained supportive. While the plans for Yucca remain law as set under Mr. Bush, Congress has never moved to fund it since.

People close to Mr. Trump, who won the Republican nomination in what amounted to a hostile takeover of the party, say he never favored the idea despite suggesting at the end of the 2016 presidential campaign that he was looking at it. But he also did not care enough to intervene as his previous energy secretary, Rick Perry, supported the measure, and as the Office of Management and Budget listed $120 million in the president’s budget to restart the licensing process of the site. It was listed as one of the administration’s priorities.

Two of Mr. Trump’s political advisers, Bill Stepien and Justin Clark, flagged Yucca Mountain early on as a political danger zone, particularly if Mr. Trump wanted to try to put Nevada in play in 2020.

But it showed up in the budget, and Mr. Perry toured the site in March 2017, shortly after he and the Energy Department were sued by the attorney general in Mr. Perry’s home state — Texas, which has been one of the few places in the country accepting low-level nuclear waste — for not licensing Yucca Mountain.

Mr. Stepien drafted a memo in May 2017 that went to top White House officials, including the chief of staff at the time, Reince Priebus, and the president’s chief strategist at the time, Stephen K. Bannon, describing Yucca Mountain as a critical issue for a number of Nevada voters, according to people familiar with its contents. The memo mentioned that Mr. Heller was facing a re-election bid in 2018.

Mr. Priebus called a meeting in his office with Mr. Stepien; Mr. Clark; Rick A. Dearborn, then a deputy chief of staff; and Mr. Perry and his chief of staff. Mr. Priebus told aides that the president did not want to move ahead with the Yucca Mountain proposal, and that they should stop talking about it. It was to come out of the budget, he added.

But Mr. Perry continued talking about it. In June 2017, he testified at a House hearing that officials had a “moral obligation” to fund the site and continue with the nuclear waste proposal.

“Listen, I understand this is a politically sensitive topic for some,” Mr. Perry testified. “But we can no longer kick the can down the road.”

An aide to Mr. Perry did not respond to emails seeking comment as to why Mr. Perry pushed the issue so aggressively despite concerns from the White House.

Mr. Perry’s advocacy was enough to agitate Mr. Dearborn, who summoned Mr. Perry to the White House and reminded him of the directive to stop discussing Yucca Mountain publicly. In the future, he said, Mr. Stepien and Mr. Clark had to be present for any related discussions.

Still, meetings about the proposal continued to be held. At one such meeting of more than 30 people at the White House complex, Mr. Clark reminded the room that Mr. Trump did not back the project, and an administration official began yelling that it would move forward anyway, according to an attendee.

It was in the last year, and after Mr. Trump’s understanding of the potential proximity of nuclear waste to his property, that the president focused on ensuring that everyone in his administration got the message about where he stood.

“Nevada, I hear you on Yucca Mountain and my Administration will RESPECT you!” he tweeted this month. “Congress and previous Administrations have long failed to find lasting solutions — my Administration is committed to exploring innovative approaches — I’m confident we can get it done!”

Yet even after that tweet, internal confusion has been evident.

At a House energy subcommittee hearing two weeks ago, Mark W. Menezes, the president’s nominee for deputy energy secretary, prompted alarm at the White House when he said, “What we’re trying to do is to put together a process that will give us a path to permanent storage at Yucca.” After White House officials expressed concern, Mr. Menezes put out a statement saying that he fully supported Mr. Trump’s decision.

Whether that will be enough to reassure Nevadans about Mr. Trump’s intentions remains to be seen.

“Nevadans aren’t going to just forget that Trump spent the first three years of his administration trying to treat the state as a dumping site,” said Rebecca Kirszner Katz, a former adviser to Mr. Reid. “Donald Trump had an opportunity to be on the right side of a major issue in a huge battleground state, and he bungled it.”

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