"No one's ever complained to me about it. We've been doing it for 10 years," Capt. J.R. Nettleton, the commander of the navy base, said.
But Nettleton agreed to move the scenes to the chapel, which he agreed was a more appropriate place, after 18 U.S. service members protested the placement of the scenes.
The members appealed to the Military Religious Freedom Foundation after holding a secret meeting, the Miami Herald reported.
"Our military members here endure many hardship," the letter to the foundation states. "When they finally have time to relax with their military family, they should not have to feel uncomfortable, out of place, or insignificant because their beliefs are not represented."
Foundation president Mikey Weinstein said 11 of the members were Christians, while the other seven included Jews, Muslims, agnostics and atheists.
Troops are generally expected to take complaints to their immediate supervisor, but Weinstein said the 18 service members feared retribution.
"There's a witch hunt going on down there at Guantánamo right now to find out who the 18 are," he said.