Heavy flooding has killed scores of people in the east African country of Malawi, where nearly a third of the country was declared to be in a state of disaster.

Malawi's President Peter Mutharika said on Tuesday that at least 48 people were killed and 23,000 others displaced in flash floods that have wreaked havoc in 10 out of 23 districts in his country.

Some of the victims died when villages were flooded in Malawi's southern Mangoche district, about 100 kilometres south of the commercial capital, Blantyre, according to Grey Mkwanda, a district planning officer.

Livestock, crops and homes were swept away by floodwaters, with some homes completely submerged.

"People have fled into schools and churches on the higher ground, others are in the open because there is not enough space," Mkwanda said.

Others died in Blantyre when their homes collapsed, according to Mkwanda.

"In some cases you cannot believe there was a house here," said Allan Ngumya, a member of parliament who represents the area.

Police are also looking for two children who went missing in Blantyre, police spokesman Elizabeth Divala said.

International aid appeal

Mutharika has appealed to the international community for assistance for the impoverished country.

"Government alone cannot afford to help so I appeal to the international community for urgent assistance," he said.

Flooding began last month and heavy rain is expected to continue, especially in the north and central parts of the country, according to Elina Kululanga, Malawi's director of meteorological services and climate change.

In neighbouring Mozambique, where some waters have risen to over double flood thresholds, a group of 25 school children was swept away by torrents on Monday, and 18 others have been reported missing.

Flooding in the two east African neighbours has left much of Malawi's centre and western border region under water, and large eastern swathes of neighbouring Mozambique swamped.

The region is likely to face at least two more days of torrential rain carried by late summer storms, according to meteorologists.