The government's declared a state of emergency, because of potential food shortages. At least 70 percent of Malawi's population are subsistence farmers.
Rainfall could continue for another two to three weeks.
Naomi Herbert, from the Anglican charity United Society (Us), told Premier: "It's just rained continually. My colleague in Malawi was trying to visit communities, and was even struggling to keep the car on the road.
"They actually had to be dug out twice, the car slipped off the mud road, and the communities they waved goodbye to had to come and rescue them.
"Malawi is prone to either having floods or droughts and with 70-80% of the population as subsistence farmers, they're very vulnerable to extreme weather conditions.
"We need to pray that the rain stops, because if it is going to continue for the next two to three weeks, it's just going to get worse and worse.
"It's also for the aftermath... the crops that were planted weren't thriving, and now they would've been washed away. So what is Malawi going to eat? How are they going to grow their crops?
"We really need to hold them up in our prayers, both in the immediate future and the long term future."
Malawi has a population of 16 million. Around 3 in 4 people in Malawi are Christian.