The lightning struck a church building at Tsangano in Ntcheu in the afternoon.
Ntcheu police officer-in-charge Aubrey Nyirenda has confired of the three deaths due to the lightning.
"Some of the casualties are admitted to Tsangano health centre," said Nyirenda.
Last week, six people were killed and two others seriously injured when lightning struck them in different places in Chikhwawa district.
Police and weather experts are warning people to take extra precautions against exposing themselves to lightning during this rainy season.
Sorry for laughing God but isnt it funny that a lightning bolt could kill a believer on a sunday in a church while attending the sunday mass? Yeah, its in Malawi... all the more funny