Is this a precedent? A message from president Jefferson Davis, dated at Richmond, Virgnia, March 9, 1864 to flag officer William F. Lynch, who commanded the Naval forces at Wilmington, makes a direct order:

"Flag-Officer LYNCH, C. S. Navy, Wilmington, N. C.:
The conduct of General Whiting and yourself, so nearly producing collision between the army and navy under your commands, is disapproved. You will without delay turn over your command to the officer next in rank, and report in person at the Navy Department.

JEFFERSON DAVIS."

I have not been able to locate this particular dispatch in the volumes of the Naval Official Records, but it is shown in series 1, volume 51, part 1, of the Army Official Records.
This conflict between the Navy and Army commanders at Wilmington must have been quite serious for the president to become directly involved. I have never come across a direct order sent by the president to one of his Naval commanders, though there may be some shown in these volumes. Usually it was the Secretary of the Navy, Mallory, or his senior clerical staff or aides, who sent such orders.
The volumes of the Army Official Records are yielding a lot of trivia on Navy personnel, which cannot be found in the Naval Official Records.