Typhoon Nanmadol struck Taiwan Monday. The island, chastened by poor response to a 2009 typhoon, has strengthened infrastructure and improved evacuation and preparation measures.
Typhoon Fanapi was the first major storm to strike the island this year and the 11th typhoon to hit China.
The former president will likely appeal the decision in what local media have dubbed the trial of the century.
President has been battered by poor handling of typhoon Morakot. His government's focus on good relations with China is unlikely to change.
The Tibetan leader said his visit to comfort typhoon survivors was purely humanitarian. But will his visit harm China-Taiwan ties?
Officials say Washington did not notify Beijing before quietly dispatching an amphibious ship and aircraft to provide humanitarian aid.
Critics say Typhoon Morakot is Ma Ying-jeou's Hurricane Katrina. He has been faulted for weak leadership in dealing with a devastating storm that killed at least 127, with hundreds still missing.
Villagers were being ferried to safety Wednesday, though heavy rains disrupted rescue efforts. A three-man crew died Tuesday when their helicopter crashed.