A joint team from the Justice Department's investigation bureau and the Environment Department were denied entry to the Shrine of the Black Nazarene in the central island of Cebu when they visited on Friday, a member said.
Security guards at the shrine, set up by a priest allegedly linked to the illegal smuggling of ivory, told investigators they would have to speak to the priest's lawyers first, said Eddie Llamedo, an Environment Department spokesman.
He conceded the team did not have a search warrant at the time an d would have to obtain the proper legal papers, possibly giving suspects time to conceal any ivory items.
Asked about the incident, Cebu archdiocese spokesman Monsignor Achilles Dakay said "the lawyers are taking care of that. We will be cooperating (with authorities) but we have church lawyers".
The shrine is maintained by Monsignor Cristobal Garcia, a priest named in a National Geographic article as giving advice on how to smuggle ivory and naming carvers who would turn it into statues.
The article has touched off a nationwide investigation into the smuggling of ivory, and particularly its use in making religious statues in this largely Roman Catholic country.
Philippine authorities on Friday said they had launched a nationwide investigation into Catholic devotees collecting religious figures made of ivory smuggled from Africa.
The probe, initially focused primarily on Garcia, has become an investigation into other owners of ivory figures, amid concerns the trade is extensive, said National Bureau of Investigation's environment division Sixto Comia.
After the National Geographic article was published, the Catholic Church revealed he had been suspended in June after the Vatican began an investigation into allegations he sexually abused children three decades ago.
Garcia, who himself is known to have a large collection of ivory statues, has been sick and confined to a hospital, keeping him out of the public eye.
Catholic statues have for centuries been made with ivory, but the church now officially condemns the practice in a bid to prevent the slaughter of elephants for their tusks.
Importing ivory has been banned in the Philippines since 1981.
The maximum penalty for possessing illegal ivory is four years in jail.