Pete Hegseth ‘butted heads’ with Navy secretary over shipbuilding and push to ignore judge’s orders before firing: reports

John Phelan repeatedly clashed with Defense Secretary Pete Hegseth before he was fired as Navy secretary — including over whether to comply with a federal judge’s order, according to a new report.

Hegseth abruptly dismissed Phelan, a former financier and Trump donor, on Wednesday, marking the second major leadership shake-up at the Pentagon during the Iran war.

"Hegseth and Phelan reportedly butted heads when Phelan refused to ignore a recent federal judge’s ruling that said punishing Senator Mark Kelly for making a video in which he reminded military officers of their constitutional duty to not to not follow illegal orders would violate his First Amendment rights,” Jennifer Griffin, Fox News’ Pentagon correspondent, reported on Thursday.

“Hegseth wanted Kelly, a retired Navy captain and former astronaut, brought back onto active duty and stripped of his rank,” Griffin said. In February, the defense secretary appealed the judge’s ruling blocking his efforts to reprimand Kelly, an Arizona Democrat.

Phelan also reportedly sparred with Hegseth over how to reboot the Navy’s lackluster shipbuilding program — amid a host of other issues that strained their relationship.

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On Thursday, President Donald Trump described Phelan as “a long time friend” who he hoped would rejoin the administration “sometime in the future.” Later, he told reporters that Phelan “had some conflict, not necessarily with Pete.”

“He’s a hard charger, and he had some conflicts with some other people, mostly as to building and buying new ships,” the president said, while seated behind the Resolute Desk.

Around the same time, Phelan released a statement saying that leading the Navy “has been the honor of my life.”

"Leadership at this level is not without its challenges,” he said, according to Axios. “Decision-making can be slowed by caution, competing equities, and internal friction.”

Hung Cao, now the acting Navy secretary, said Thursday evening he is “grateful to President Trump and Secretary Hegseth for the opportunity to serve,” adding that he appreciates Phelan’s service.

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Phelan’s 13-month tenure at the Navy came to an end, seemingly out of the blue, on Wednesday evening.

A Pentagon spokesperson released a cryptic statement saying that Phelan, the 79th Navy secretary, would be departing the administration “effective immediately,” without providing any explanation.

A few hours later, a senior administration official told The Independent that Phelan had been fired.

“President Trump and Secretary Hegseth agreed new leadership at the Navy is needed,” the official said. “Secretary Hegseth informed John Phelan of this news prior to it being made public.”

The Independent has contacted the Pentagon for comment.

Beyond his clashes with Hegseth over judicial orders, the former Navy chief also stirred controversy due to his tight-knit friendship with the president.

The Harvard Business School graduate and founder of a Palm Beach-based investment firm reportedly helped raise millions for the president’s re-election campaign. The president tapped Phelan, who did not serve in the military, to lead the Navy shortly after his re-election.

Since then, the pair have kept in close contact, according to The Wall Street Journal. They regularly chatted at Mar-a-Lago, and Phelan would text the president late at night about shipbuilding.

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Senior Pentagon officials grew particularly annoyed last year when Phelan took his proposal for a new battleship directly to the president, leaving Hegseth out of the loop, sources told the outlet.

Phelan’s plans for a new class of battleships also may have contributed to his ouster, The New York Times reported.

Trump had repeatedly expressed his desire to manufacture a new fleet of warships — and Phelan had struggled to deliver on the president’s aggressive and “nearly impossible” schedule, the outlet reported.

His firing comes as the U.S. Navy is enacting a blockade in the Strait of Hormuz amid the ongoing war with Iran, which has engulfed the Middle East in violence and led to a surge in global fuel prices. Multiple recent polls show most Americans are opposed to the conflict.

Earlier in the war, on April 2, Hegseth fired Army Chief of Staff Gen. Randy George. A source familiar with the matter told CBS News that the defense secretary wanted someone in the role who would implement his and Trump’s “vision for the Army.”

Since taking the helm of the Pentagon 15 months ago, Hegseth has dismissed roughly 34 military officers, some of whom were four star generals and admirals.

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