Economy, Trade and Industry Minister Akira Amari also said he believed the summits were effectively cancelled as the rescheduled January dates would not suit all the leaders.
The abrupt postponement of the ASEAN and East Asia summits "surely lowered the credibility of the Philippine government," Amari wrote on his blog.
"Officials concerned actually see the summits as de facto called off, considering the tight schedules of national leaders in the next six months," Amari said, in unusually blunt remarks about a friendly nation.
President Arroyo made a last-minute decision Friday to postpone the two summits in Cebu, citing an approaching typhoon.
The announcement came amid fears of a terrorist attack as Britain, Australia, the United States and other nations had warned against travel to Cebu.
"Considering the size of the typhoon and that it passed by Sunday morning, the reason for the rescheduling was difficult to understand," Amari wrote.
"(Philippine) media have reported the real reason might have been the warnings of a high possibility of terrorist attacks, released not only by Britain but also the United States immediately before the events," he said.
"It is extremely dangerous in security terms for leaders from 16 nations to gather at a hotel in Cebu, which is packed with tourists."
He contrasted the Philippines to communist Vietnam, which was host to the 21-nation Asia-Pacific Economic Cooperation (APEC) summit last month.
"The difference between the Philippines and Vietnam, which banned the entry of people not related to the APEC forum, was as clear as daylight," he said.
Japanese Prime Minister Shinzo Abe went ahead with a shortened visit to the Philippines and held talks in Manila with Arroyo.
Reports have said Abe is unlikely to attend the postponed summits due to plans to visit Europe and parliamentary commitments.
Japanese foreign ministry officials refused to confirm the reports, saying the Philippine government was arranging the postponed events.