The worst of the floods hit Kunene province on Wednesday covering about 72,000 hectares (178,000 acres) of land with up to two metres (6.5 feet) of water, TPA television reported.
"In almost all areas around town things have worsened," TPA quoted Kunene's national protection services co-ordinator Goncalves Namweya as saying.
Last month, some 10,000 people were displaced when three southern Angolan provinces were hit by heavy rains after a long drought.
Several countries in the southern Africa have been plagued by flooding since the start of the rainy season in December. An estimated 100,000 people were affected in Mozambique, where 10 people died in flooding and dozens more of related diseases.