The cross was put up on Veterans Day as a memorial to four Marines killed in combat in Iraq and veterans in general, the Los Angeles Times reported Tuesday.
The Military Association of Atheists and Freethinkers protested to base officials it violates the Constitution after reading an article about the cross in the Times.
Military officials said the raising of the cross was a private undertaking by Marines and a retired Navy chaplain who served with the four dead Marines. It was not an official act or sanctioned by the Marine Corps.
"Camp Pendleton legal authorities are researching and reviewing the issue in order to make a judicious decision," the Marine Corps said in a statement released Monday. "As Marines, we are proud to honor our fallen brothers and are also proud of our extended Marine Corps family."