Trump's statement came just one day after the Navy launched a procedure that could end with Edward Gallagher and three other members of his unit being stripped of their Trident pins - effectively booting them from the SEALs.
"The Navy will NOT be taking away Warfighter and Navy Seal Eddie Gallagher’s Trident Pin. This case was handled very badly from the beginning. Get back to business!" Trump tweeted.
In July, the 40-year-old Gallagher was acquitted of charges related to the stabbing death of a wounded Islamic State prisoner in Iraq in 2017, attempted murder of other civilians and obstruction of justice.
But he was convicted of a lesser charge - posing with the slain fighter's body in a group picture with other SEALs - and demoted one rank, from chief petty officer to petty officer first class.
Last week, Trump reversed the demotion and granted clemency to Gallagher, whose case had been championed by Fox News, which the president follows closely.
A panel of Navy SEAL officers had been set to convene in December to decide whether Gallagher can remain in the unit.
It was to deliver an opinion to the commander of the US Navy's special forces, who would then make a recommendation to naval command, which has the final say.
The intervention by Trump - commander-in-chief of the US military - throws that process into doubt.
Also last week, Trump dismissed a second degree murder conviction against Army First Lieutenant Clint Lorance, who was six years into a 19-year term for ordering soldiers in 2012 to fire on three unarmed Afghan men on a motorcycle, two of whom died.
He also granted clemency to West Point graduate Matt Golsteyn, an ex-member of the elite US Army Green Berets, charged with premeditated murder in the shooting death of an alleged Taliban bomb-maker in 2010.
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