The company said the mine site recorded 500mm of rain in the past five days. Annual rainfall averages 450mm.
Normal operations are expected to resume in about a week, subject to the water receding.
Vele has 5500 tonnes of thermal coal stockpiled and normally produces 7000 saleable tonnes per week.
The miner’s nearby lodge and management facility has been in use as a crisis communications hub. It is also a safe haven for people stranded near the Mapungubwe World Heritage Site and surrounding farms.
Doctors Without Borders, the South African police and the Musina local municipality have set up base in the area, where more than 150 flood victims are expected to seek shelter.
Vele began production early last year , with 13,600 tonnes of coal mined in January and February.
