In his remarks, Milley said his presence with President Trump sent the wrong message to the military and the nation.
"We must hold dear the principle of an apolitical military that is so deeply rooted in the very essence of our Republic," Milley said in his speech.
Milley finished by telling graduates of the National Defense University to 'embrace the Constitution.'
"Keep it close to your heart. It is our North Star. It's our map to a better future," Milley said.
Milley's apology fell short with some Democrats in Congress, who argue the military did not stand up to the President in real time.
Milley's statement came as President Trump again expressed satisfaction with the push to clear Lafayette Square.
“Our great National Guard Troops who took care of the area around the White House could hardly believe how easy it was,” the President wrote on Twitter.
“'A walk in the park,' one said,” the President added.