Heavy rains from late December and through most of January have led to floods in the two countries, with torrential downpours at the weekend again swelling rivers.
South Africa’s Cooperative Governance Ministry estimated at least 32 have been killed while police said on Monday another seven went missing in Centurion, near Pretoria, after they were swept away by high waters.
The army has been placed on stand-by to evacuate people from areas near major dams.
“All disaster management structures in the country have been put on high alert,” the cooperative governance ministry said.
South African logistics group Transnet said last week heavy rains had disrupted its freight rail operations, affecting coal and maize exports.
South Africa’s 2009/10 maize surplus is likely to prevent any supply shortage of the grain this year but the extremely wet conditions may have an impact on the soy bean and sunflower harvest, the chief executive of farmers’ group Grain SA told Reuters in an interview last week.
In Mozambique, about 13,000 people have seen damage to the their homes or been evacuated due to floods and heavy winds, state-run Radio Mozambique reported on Monday.
At least 10 have been killed in the country.