The Norfolk Naval Shipyard in Portsmouth, Virginia, has lowered the Confederate flag that flew on its grounds for decades, the Virginian-Pilot reported Monday. The banner came down Friday amid a nationwide backlash against Confederate symbols following the Charleston church massacre.

The flag -- which was not the familiar stars-and-bars design of the battle flag -- had flown over the side gate of the historic Norfolk Naval Shipyard since 1967. The shipyard in Norfolk is charged with repairing and modernizing ships and is the U.S. Navy's oldest and largest industrial facility, according to the facility's website.

There was no military policy on displaying the Confederate flag, but it was removed amid a nationwide debate after Dylann Roof, the accused killer of nine African-Americans in the Emanuel AME Church in South Carolina, was found to have repeatedly posed with the flag.

The shipyard in Portsmouth served the Confederate States during the Civil War and was called the Gosport Shipyard before it was destroyed in 1862 and rebuilt as the Norfolk Naval Shipyard. The Confederate flag at the shipyard -- the first design with seven stars representing the original seceded states -- was first put up on the 200th anniversary of the facility in 1967, flying alongside the American, British and Virginian flags or the "four sovereign flags" of Virginia, according to an article on the Navy's website cited, via the Virginian-Pilot. That time was also the height of the civil rights movement, when several Southern states adopted Confederate imagery. An anonymous Navy official told the paper it was the only naval shipyard to fly a Confederate flag. On Friday, that changed.

All four flags above the shipyard's side gate were taken down and moved to a museum. The facility's commander, Capt. Scott Brown, reportedly ordered the move in the best interest of the facility and the Navy. While the flag was reportedly intended to represent the 248-year history of the shipyard, modern times called for a change.

"The flags represent progress, progress in shipbuilding, progress in repair and progress in the defense of our country," facility spokeswoman Terri Davis told the Virginian-Pilot. "Removing the flags from the gates doesn't diminish their historical significance, but it does allow us to focus on successful execution of our mission."

On Sunday night the shipyard tweeted and posted to Facebook about the removal. A picture showed the gate featuring four American flags with the message, "We are America's Shipyard! United we stand under one flag."

The Confederate battle flag was removed from South Carolina's Statehouse grounds earlier this month. It also was removed from a government building in Tampa, Florida, while pro-flag gatherings in Oklahoma greeted a visit from President Barack Obama.