About 40 people had gathered in the Church of Central African Presbytery in Mzimba, about 300km north of the capital Lilongwe, when lightning struck on Saturday afternoon, said Fletcher Ndhlovu, an elder of the church.
"It started raining heavily about 14:00 when strong lightning struck the church building, sending everybody into shock," Ndhlovu told AFP.
The victims were taken to the district hospital "where 11 people were pronounced dead on arrival," said Mzimba hospital physician Barton Jere.
"The persons arrived here when they were already dead but we admitted eight people and 10 others were treated as out patients," Jere told AFP.
"They were all in a state of shock."
This was one of the highest death tolls from a lightning strike in recent years in Malawi, which is now in the rainy season.