The crosses were placed as memorials to fallen troops.
Atheist groups protested, saying the separation of church and state dictates religious symbols should not be allowed on public land, the San Diego Union Tribune reported Monday.
A group called Military Association of Atheists and Freethinkers filed an objection with the base.
Camp Pendleton officials said they conducted a legal review and sent their recommendation to Washington for a final decision.
They declined to say what that recommendation is, the Union-Tribune reported.
Jason Torpy, the president of the military atheist association and a West Point graduate and former Army captain, said he has no doubt that the crosses are unconstitutional.
He has no problem with a memorial on the hill, he said, as long as it doesn't involve a Christian symbol.
A flag, plaque or a wall would be appropriate, he said.