Both men face a maximum punishment of life in prison without the possibility of parole if convicted.
The New York Times first reported on Saturday that Navy Secretary Richard Spencer and Rear Adm. Collin Green had effectively given Trump an ultimatum that could cost them their careers.
"The Navy follows the lawful orders of the President," Rear Adm. Charlie Brown said. "We will do so in case of an order to stop the administrative review of SOC [special operations chief] Gallagher's professional qualification."
President Donald Trump has nixed any effort by the Navy to excommunicate Eddie Gallagher from the SEAL community
"I had a robust discussion with the president yesterday and I offered – as I do in all matters – the facts, the options, my advice, the recommendations and we'll see how things play out."