Rt Revd David Lai also said the Episcopal Church is gathering information on which churches are damaged, so it can respond.
He especially referred to churches in the hills and mountains of Taiwan, for example aboriginal churches, which are often less stable and more exposed.
He also said Typhoon Soudolor could be the worst to have ever hit Taiwan.
At least 100 people have been injured so far from the typhoon, which struck in the early hours of Saturday and is still raging.
Two million homes are currently without electricity. Buildings have fallen down and some areas are completely flooded or affected by landslides.
Rt Revd Lai told Premier: "The National Climate Report supposed this is the strongest typhoon on the Earth. And according to NASA, the satellites made sure the typhoon is very strong.
"So far we're still trying to collect exact information about the damage of the church, because some aboriginee's churches' are on the mountain area.
"I am still in prayer, and we ask our church members to watch and to pray for God's mercy.
"Just pray. Almighty God, He knows how to help us, how to protect us. We expect and we believe God will use his way to breaking [sic] us."
Listen to Premier's Aaron James speaking to Rt Revd David Lai here:
