Panicked residents have drowned or been killed by crocodiles as they attempted to cross rivers for higher ground.
With no sign of a let-up in the rainy weather, there are growing fears the flooding could worsen in the coming weeks and devastate the largely agricultural-based economies of the region in the middle of the critical summer growing season.
Heavy downpours are common in southern Africa in the rainy season, which runs generally from November to April, but the relentless rain is unusual and has caught officials off guard.
Zambia's government has appealed for $13 million in emergency funds from Western donors to cope with the crisis.
Authorities have closed schools, converting them into shelters for those displaced. Many refugees have been living in tents provided by the government and relief agencies.
In Malawi, overflowing rivers swamped agricultural areas that had experienced food shortages in the past as a result of floods, displacing hundreds.
Mozambique, which has resisted asking for foreign assistance, was bracing for more heavy flooding one day after the amount of water in the Limpopo river, one of its largest, rose to alarming levels.
Waters also began rising in Mozambique's Zambezi valley weeks ago, as unseasonably heavy rains forced the Zambezi River to swell.
The government has evacuated people from areas initially deemed safe but now considered dangerous.
UN agencies have warned the flooding there could be worse than in 2000-2001, when 700 people died and another half a million became refugees.