Flooding from heavy rains have killed at least 40 people in Mozambique and neighbouring Malawi, where a state of natural disaster was declared Tuesday in nearly a third of the country.

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

Malawi officials said at least 19 people have died there, and nearly 3,900 homes have had to be abandoned.

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.

Roads and rail lines have been cut by flooded rivers, which according to officials have also swept away surprised bystanders, people seeking to flee rising waters in canoes and sleeping families whose homes were suddenly overcome by rushing torrents.