Malawi deployed military helicopters and boats Thursday in a bid to rescue desperate flood victims stranded on patches of high ground after raging waters killed at least 48 people and left 100,000 homeless.

Vice President Saulos Chilima said the rescue operation had been delayed because of poor weather over the two previous days and helicopters were struggling to land because of the high water levels.

"Around 800 people have been rescued from the flooded areas in (the southern districts of) Nsanje and Chikwawa," he said in a statement, adding that more support such as boats, helicopters, tents and food was urgently needed.

The two districts were the worst hit by the floods which have ravaged half of the 28 districts in t14he poor southern African nation, with neighbouring Mozambique also battling the rising waters.

"We are racing against time to rescue everybody. We want to make sure everybody is safe," Chikwawa district commissioner Alex Mdoko told AFP.

Scores of people in the district were feared dead after being swept away by the floods, he added.

A number of canoes carrying rescued villagers capsized due to overloading on the Shire river.

Five major roads in the south were closed after bridges were washed away.

Malawi's power generating company Escom shut down its main hydro plant on the Shire River due to debris accumulating in the turbines, leading to power blackouts in the commercial capital.

President Peter Mutharika has called the floods a "national tragedy that urgently needs both local and international response".

Across the border in Mozambique, 300,000 people across four provinces in the centre and north of the country found themselves without electricity when power lines collapsed in the flood waters.

"Two provinces are affected by the floods," National Institute of Disaster Management spokeswoman Rita Almeida told AFP.

Initial reports suggested 16 people had died in Mozambique, though Almeida could not confirm this.

In the Licungo River basin in the centre of the country, 19,000 people have been displaced by the rising waters, she said, while in the Lurio River Basin further north, 16,300 people were affected.

According to local newspaper A Verdade, the town of Cuamba near Mozambique's border with Malawi has been completely cut off by the floodwaters.

And while Mozambique's Meterological Institute said rain had eased off on Thursday, disaster management remained on high alert.

The country's deadliest floods were in 2000 when about 800 people were killed.