“In the meantime, we will continue to treat all of our personnel with respect,” said Gen. Joseph F. Dunford Jr., chairman of the Joint Chiefs of Staff.

The lack of clear direction from officials left the status of thousands of active transgender service members in limbo, one day after President Trump’s sudden announcement on Twitter. Dunford’s message to his troops suggested that those in leadership roles were caught off guard, despite Trump’s insistence that he was implementing the ban at the behest of the military.

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“I know there are questions about yesterday’s announcement,” began Dunford’s letter to the heads of the military ­branches as well as commanders and senior enlisted leaders.

The rollout of Trump’s new policy was bumpy from the start. While it has received praise from some Republicans, it has also antagonized some in the party. Several Republicans have refused to say whether they support the president.

On Thursday, House Speaker Paul D. Ryan (R-Wis.) declined to back the ban and said he wanted to see what the Pentagon and the White House produced in their review. Several Republicans, including Sens. John McCain (Ariz.), Joni Ernst (Iowa) and Orrin G. Hatch (Utah), on Wednesday criticized the president’s decision.

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“I don’t think we should be discriminating against anyone,” Hatch said. “Transgender people are people, and deserve the best we can do for them.”

Adding to the confusion, Defense Secretary Jim Mattis was on vacation this week. The secretary, who had only weeks ago asked for more time to review the policy, was informed of Trump’s decision Tuesday.

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With Mattis out, chief Pentagon spokeswoman Dana W. White released a statement Thursday that the Pentagon was “awaiting formal guidance from the White House as a follow-up” to Trump’s announcement. White promised there would be “detailed guidance” from the Pentagon in the “near future” on how the policy change would be implemented.

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White House spokeswoman Sarah Huckabee Sanders offered no new information during a press briefing, repeating that the White House would work with the Pentagon to implement the plan.

“Like I said, they’re going to have to work on the details as it all moves forward to lawfully implement that policy change from this point,” she said.

A 2016 Rand Corp. study commissioned by the Pentagon estimates that there are about 11,000 transgender troops in the reserves and active-duty military.

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Trump’s decision went further than anything under consideration by the Pentagon, which was nearing the end of its review on its transgender policy.

Since President Barack Obama lifted the ban on transgender troops in June last year, hundreds of service members have come out and are serving openly. The only part of Obama’s policy the Pentagon was still reviewing was whether the military would admit recruits who identified as transgender. The question of transgender active-duty members appeared to have been settled.

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The Obama policy would have allowed the recruits to begin serving July 1, but Mattis delayed that change the day before the rule was to set in, saying more review was required.

The six-month delay would have allowed a further review of how integrating transgender recruits would affect the military’s “readiness and lethality,” Mattis said in a memo last month. That review was due Dec. 1.

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Trump’s ban is also wider-ranging than what many conservative House members were seeking as they debated a new defense spending bill. These lawmakers had sought to prohibit the Pentagon from covering the cost of gender transition therapies for active-duty service members. They did not seek a blanket ban on transgender service members.

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Rep. Vicky Hartzler (R-Mo.) contacted Mattis and the White House before filing an amendment to the defense spending bill barring transgender service members from receiving gender reassignment therapy, according to a GOP congressional aide familiar with the conversations. While Hartzler’s office had heard from some Pentagon staffers on the issue, it was not until the day of the vote that Mattis returned Hartzler’s phone call, the aide said. Mattis did not give Hartzler a clear answer on the Pentagon’s plans on this issue, and so Hartzler went forward with her amendment, which ultimately failed.

The amendment’s demise led House GOP members to lobby the White House directly. The impasse threatened military spending, but most important for Trump, it potentially held up money that had been appropriated for the border wall between the United States and Mexico, a key promise he had made during the campaign.

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Hartzler praised Trump’s announcement Wednesday, saying on Twitter, “President Trump’s decision . . . has the best interests of the #military in mind, and I thank him for taking action.”

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Trump’s intervention potentially sends the Pentagon back to the drawing board on an issue that had already required years of review and discussion.

Aaron Belkin, director of the Palm Center, a think tank that has helped the Pentagon research transgender people serving in the military, said in a statement Wednesday that the change would bring about something worse than the “don’t ask, don’t tell” policy barring gay troops from serving openly that was repealed in 2010.

“This is a shocking and ignorant attack on our military and on transgender troops who have been serving honorably and effectively for the past year,” Belkin said.

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Critics of the decision also say that the cost to cover medical treatments for transitioning service members would be a tiny fraction of the Pentagon’s overall budget. The Rand study estimated that gender-transition-related medical treatments would cost the military between $2.4 million and $8.4 million annually.

Jenna Johnson, Karoun Demirjian and James Hohmann contributed to this report.