"There is a trend of rising protectionism that the EU is using to threaten to block some of our exports, including citrus exports," he said on Sunday, during an unofficial meeting with South African diplomats at his home in Belgium's capital, Brussels.
"We are concerned about this. We will speak of this at the meeting and see how we can find a solution."
Citrus imports were halted after some shipments were found to have the citrus black spot (CBS) disease.
The spot is a fungal disease which affects the external appearance of the fruit.
The South African delegation from the international relations department arrived in Brussels on Saturday ahead of bilateral talks and political engagement.
They are accompanying Minister Maite Nkoana-Mashabane, who is due to meet with several top European officials this week. The accompanying officials met with the ambassador on Sunday.
Nkosi said the citrus sector contributed around R6-billion to South Africa's gross domestic product (GDP).
CBS a phytosanitary measure
The rise in citrus production was mainly due to the increase in cultivation areas, packaging and transport improvements, and preferences for healthier food options.
But citrus harvesting and production in most of Europe continues to decline, particularly at this time of the year due to climate conditions.
About 40% of South Africa's citrus exports go to the EU, making it one of the country's most important markets. South Africa is the world's biggest exporter of whole oranges and the largest shipper of grapefruit.
"This is a big business," said Nkosi.
In 1993, the EU declared CBS a phytosanitary measure, meaning it was placed on a trade watch-list at EU borders. If spotty fruit were found, the consignment would be impounded.
This reduced the proportion of citrus exports to the EU. Farmers are now spending substantial amounts to get rid of the spots.
The Citrus Growers' Association of Southern Africa listed nine additional direct and indirect costs associated with the EU measure. These include more spraying, replanting earlier than necessary, added inspection costs, and storage costs for impounded fruit at European ports.
Export earnings account for about 80-90% of citrus growers' revenue. The industry wants the phytosanitary measure withdrawn pending further research into black spot. Farmers believe the threat of citrus fruit being blacklisted could have disastrous effects on the sector.
The first case of CBS was recorded in 1929, and until recently the EU has not been too concerned about excluding spotty fruit.
Nkosi said the EU remained one of South Africa's biggest trading partners, accounting for 24% of global exports.
He said the eurozone financial crisis had significantly reduced demand for South African exports.
Despite its problems, Nkosi said the EU remained the second-largest economy in the world, accounting for 17% of the world's GDP.
"Our relations with the EU go a long way," he said.
"South Africa is the only African country with a partnership with the EU."
'EU can no longer help'
However, Nkosi was concerned that EU development aid to South Africa would be significantly cut in the coming years.
"We need to be alive [to this], and the reality is the EU can no longer help us the way they used to," he said.
Despite this, he said the EU would remain a strategic partner. – Sapa