The parcels - worth R500 each - contain staple food, blankets, eating utensils, water purification tablets and plastic sheets, the organisation's founder Imtiaz Sooliman said on Saturday.
The eight-member team reached areas more than 100km away from Blantyre, according to Sooliman, and distribution will also be carried out in Chikwana, Nsanje, Mangochi, Machinga, Balaka, Zomba, Phalombe and Mulanje regions.
Continuous rain and the "baby" Cyclone Bansi have resulted in Malawi declaring 15 of the 28 national districts disaster zones. Malawi has called for international assistance. An estimated 100,000 people have been left homeless and 173 are confirmed dead.
The death toll is expected to rise as it is believed that 183 people have been swept away from one village alone.
Sooliman said the southern African country was probably facing the "greatest flood disaster in the history of its existence".
"Massive destruction to agriculture, roads, bridges and general infrastructure, including power facilities, has complicated the situation due to prolonged power outages.
"The Malawi defence force has already rescued more than 4,000 people with the fear that many more are trapped in inaccessible areas," said Sooliman.
There are also concerns of a cholera outbreak and other water-borne diseases as there is no clean drinking water and the sewerage system is contaminated.
The humanitarian crisis will be made worse as tropical Cyclone Chedza hit Malawi on Sunday.
"It is expected to be far more destructive than Cyclone Bansi, bringing more heavy rains and greater flooding," said Sooliman, who urged South Africans to contribute to the relief efforts.
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