Antonio Fernando spoke on Saturday at the end of a three-day meeting for southern African cotton producers held in Mozambique's capital, Maputo, to plan how to revive the cotton industry in the region.
He claimed that the subsidies negated the efforts of Africans and that the initiatives of peasant farmers to improve their competitiveness.
They "have purely and simply been annulled by the subsidies granted by industrialised countries in favour of their own producers", he said.
"As a result, cotton prices on the world market do not reflect the costs of production," he said.
Fernando called for export subsidies to be stopped and for measures to be introduced in support of cotton producers in developing countries.
Poor countries had to export raw cotton to rich countries, and then import from those countries shirts, trousers, linen and other items made from cotton, he said.
The difficulty in placing African products in northern markets "hits at the income of our farmers, who are working under much more difficult conditions than producers in the developed countries", Fernando said.
According to documentation distributed at the workshop, the world market price of cotton has slumped by 54% since the mid-1990s, posing a serious threat to 3 million cotton producers in southern Africa.
Prices are depressed essentially because farmers in the developed world, subsidised by their governments, dump ever larger amounts of cotton on the international market.