Eddie Gallagher stands accused of stabbing to death a wounded prisoner of war and shooting at innocent civilians, according to The Navy Times.
In a tweet on Saturday morning, Mr Trump indicated Gallagher would be moved to more comfortable accommodation.
"In honor of his past service to our Country, Navy Seal #EddieGallagher will soon be moved to less restrictive confinement while he awaits his day in court," he wrote
"Process should move quickly!"
Mr Trump appears to be responding to a request from a number of congressmen for the Navy to review the conditions of Mr Gallagher's confinement.
His tweet comes after Republican congressman Ralph Norman of South Carolina tweeted that he had spoken to the president over the phone about moving Gallagher.
In a later tweet, he wrote: As I've said from the start, I believe Chief Gallagher will soon have a fair and impartial trial.
"But until proven otherwise, it's appropriate that he be treated as a decorated soldier who still has the presumption of innocence."
Mr Gallagher, 39, is currently jailed at the Naval Consolidated Brig Miramar military prison in California and is facing multiple charges of war crimes.
The 19-year Navy veteran is accused of stabbing to death a wounded 15-year-old Islamic State fighter who was in his care, according to a charge sheet obtained by CNN.
he is also allegedly charged with shooting at innocent civilians and posing for an unofficial picture "with a human casualty".
In addition, he is charged with flying a drone over a human casualty and wrongfully possessing and using the painkiller Tramadol Hydrochloride, according to the charge sheet obtained by CNN.
Mr Gallagher has pleaded not guilty to all the charges.
Additional reporting by AP
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