Two Malawian soldiers went missing after their rescue boat was swept away on Tuesday in the southern Mulanje area.
The New York Times quotes a military spokesperson as saying that the mission was hampered by a swollen river.
The soldiers were part of a six-member crew that went to rescue people stranded after Tropical Storm Freddy ripped through the region, Minister of Local Government Richard Chimwendo Banda told a local outlet.
Two other soldiers and one civilian managed to swim back after the boat malfunctioned on the way to the rescue mission, the minister told Zodiak Online.
Mr Banda said one of the missing soldiers was spotted on a tree and efforts were ongoing to rescue him.
Tropical Storm Freddy, a record-breaking storm that barrelled into the landlocked south-east African nation over the weekend, has left more than 200 people dead.
Malawi’s commercial hub, Blantyre, has recorded most of the deaths, including dozens of children.
Authorities have delayed school reopening to Friday and declared a state of disaster in 10 southern districts that have been hardest hit by the storm.