At least 80 domestic flights have been canceled.
Aquino said army troops deployed search and rescue boats in advance. Authorities ordered small boats and ferries not to venture out along the country's eastern seaboard, warning of rough seas and torrential rain and wind that could whip up four-meter (13-foot) waves.
In the mountainous Compostela Valley, authorities halted mining operations and ordered villagers to evacuate to prevent a repeat of deadly losses from landslides and the collapse of mine tunnels seen in recent storms.
Residents in a riverside village that was wiped out by the storm last December in southern Cagayan de Oro city moved to a government hall, carrying TV sets, bundles of clothes and a pig.
Nearly 8,000 villagers were moved to four government shelters in Hinatuan, the coastal town that was directly in Bopha's path until the typhoon began to veer slightly, officials said.
Bopha, a Cambodian word for flower or a girl, is the 16th weather disturbance to hit the Philippines this year, less than the 20 typhoons and storms that normally lash the archipelago annually. Forecasters say at least one more storm may hit the country before Christmas.
Associated Press writer Teresa Cerojano contributed to this report.