The French Polynesian president, Oscar Temaru, has personally removed the wooden cross placed on the wall inside the territorial assembly building in Papeete.
The Catholic speaker, Antony Geros, installed the crucifix shortly after his election in June, saying it would bless the proceedings with an atmosphere of union, harmony and calm.
But Tahiti Presse says the move was controversial and seen as in defiance of French law.
It was also criticised by the territory's main congregation, the Maohi Protestant church, and by members of the new ruling coalition.
Mr Geros has accepted the removal of the cross, saying its placement was his personal initiative.
He went on to say that the cross is the statutory sign of his Tavini Huaratira Party, the main party within the ruling majority.