Navy Secretary John Phelan was fired on Wednesday after months of infighting with senior Pentagon leaders and disagreements over how to revive the Navy’s struggling shipbuilding program.

Mr. Phelan is leaving the Pentagon and the Trump administration effective immediately, wrote Sean Parnell, the Pentagon’s chief spokesman, in a terse statement.

In his role leading the Navy, Mr. Phelan had championed the “Golden Fleet,” a major investment in new ships including a “Trump-class” battleship. But Mr. Phelan’s leadership was marred by feuds with senior leaders in the Pentagon, including Defense Secretary Pete Hegseth and Deputy Defense Secretary Stephen Feinberg, Pentagon and congressional officials said.

Mr. Phelan is the first service secretary to leave the administration, though he is the second one to clash with the defense secretary. Mr. Hegseth also has butted heads with Army Secretary Daniel P. Driscoll over promotions and a host of other issues. Mr. Hegseth fired the Army’s chief of staff, Gen. Randy George, earlier this month.

The Navy secretary has no role overseeing deployed forces, and Mr. Phelan’s firing is not likely to have significant implications for the conduct of the Iran war or U.S. Navy operations to blockade Iranian ports or open the Strait of Hormuz. As the Navy’s top civilian leader, his main responsibility is to oversee the building of the future naval and Marine Corps force.

But the tumult could make it harder for the Navy to replenish its stock of Tomahawk missiles and high-end air defense systems, which have been in heavy use in Iran.

Tensions had been simmering for months between Mr. Phelan and his two bosses — Mr. Hegseth and Mr. Feinberg — over management style, personnel issues and other matters.

Mr. Feinberg, in particular, had grown increasingly dissatisfied with Mr. Phelan’s handling of the Navy’s major new shipbuilding initiative, and had been siphoning off responsibility for the project from him, said the congressional official, who spoke on the condition of anonymity to discuss personnel matters.

Mr. Phelan, a White House appointee, also had a contentious relationship with his deputy, Under Secretary Hung Cao, who is more aligned with Mr. Hegseth, especially on some of the social and cultural battles that have defined the defense secretary’s tenure, the officials said.

A senior administration official said that Mr. Hegseth informed Mr. Phelan before the Pentagon’s official announcement that he and President Trump had decided that the Navy needed new leadership.

A spokeswoman for Mr. Phelan referred all questions on Wednesday evening to the Defense Department.

Last fall, Mr. Hegseth fired Mr. Phelan’s chief of staff, Jon Harrison, who had clashed with senior officials throughout the Pentagon. The unusual move highlighted the broader tensions between Mr. Hegseth and Mr. Phelan.

Still, the timing of Mr. Phelan’s firing caught some Pentagon and congressional officials off guard. On Wednesday, Mr. Phelan was making the rounds on Capitol Hill, talking to senators about his upcoming annual hearing with lawmakers to discuss the Navy’s budget request and other priorities.

“Secretary Phelan’s abrupt dismissal is troubling,” Senator Jack Reed of Rhode Island, the top Democrat on the Armed Services Committee, said in a statement Wednesday night. “In the midst of President Trump’s war of choice in Iran, at a moment when our naval forces are stretched thin across multiple theaters, this kind of disruption at the top sends the wrong signal to our sailors and Marines, to our allies, and to our adversaries.”

Mr. Phelan also had a close relationship with Mr. Trump. In December, Mr. Phelan appeared alongside Mr. Trump at his Mar-a-Lago resort to announce the “Golden Fleet” and the new class of battleships bearing Mr. Trump’s name.

“John Phelan is one of the most successful businessmen in the country — in our country,” Mr. Trump said. “He’s been a tremendous success.”

Before joining the Trump administration, Mr. Phelan ran a private investment fund based in Florida.

“He’s taken probably the largest salary cut in history, but he wanted to do it,” Mr. Trump said at the December press conference. “He wants to rebuild our Navy. And you needed that kind of a brain to do it properly.”

But Mr. Trump’s effusive praise masked deeper tensions with Mr. Phelan’s Pentagon bosses.

Bryan Clark, a naval analyst at the Hudson Institute, said that Mr. Phelan was “driving the Navy in a different direction” than what Mr. Hegseth and Mr. Feinberg wanted.

“He was championing initiatives like the battleship and frigate that don’t align with where the D.O.W. leadership is taking the military, which is toward submarines, stealth aircraft, unmanned systems and software-driven capabilities like electronic warfare and cyber,” Mr. Clark said in an email, using the abbreviation for Department of War, as the administration calls the Defense Department.

Mr. Phelan also clashed with Mr. Hegseth over personnel issues in the Navy and Marine Corps, a former senior military official said. Mr. Hegseth has directed service secretaries to scrub the social media accounts of general- and admiral-level promotion candidates to ensure they are not deemed too “woke” by Mr. Hegseth’s standards, the official said.

Maggie Haberman and Eric Schmitt contributed reporting.