The cult was held responsible for a nerve gas attack on a Tokyo subway station in 1995 that killed 12 people and injured hundreds.
Immigration Commissioner Alipio Fernandez said Koichi Ninomiya and Hiroki Tsuno would be denied entry if they attempted to visit the country. He said he had received reports that the two were scheduled to visit Manila within the next few days.
"The government cannot take chances by allowing the entry of aliens who are considered threats to our peace and security," Fernandez said in a statement.
The Philippine embassy in Tokyo had earlier warned that the two were planning to visit the country this week and stay for two days, the Bureau of Immigration said. It did not specify the reason for their planned visit.
Ninomiya and Tsuno previously visited Manila separately, the bureau’s records showed. They are alleged to be ranking members of the Aum cult.
Followers of the cult — whose leader Shoko Asahara was sentenced to death in February — have set up more than 10 companies nationwide, including software makers.
Aum Shinrikyo, which has changed its name to Aleph and remains under close surveillance by Japanese authorities, claims the businesses are intended to raise funds to compensate victims of the subway gassing and other cult crimes. — Jose Aravilla, wire reports