"Today, I directed my staff to begin crafting an order that would prohibit the Confederate battle flag from all public spaces and work areas aboard Navy installations, ships, aircraft, and submarines", Gilday said via Twitter on Tuesday.
"The order is meant to ensure unit cohesion, preserve good order and discipline, and uphold the Navy’s core values of honor, courage, and commitment", Gilday said.
On 9 June, US Army spokesperson Lieutenant Colonel Emanuel L. Ortiz announced that the Army will consider renaming bases that honour Confederate leaders.
Some Americans view the Confederate flag with pride in their heritage and a reminder of the states' rights in the US federation. However, others associate it with slavery and racism at the time of the Civil War, and later expression of the policies of segregation of African-Americans in the United States as well as with treason.
Gilday issued the message as nationwide protests continued prompted by the death of African-American George Floyd in police custody.