They have been stuck at European ports after new EU import regulations were suddenly imposed in July.
The new requirements are aimed at tackling the potential spread of the false codling moth, which is native to sub-Saharan Africa.
This requires South African farmers to keep fruit at extremely cold temperatures of two degrees Celsius or lower for 25 days, AFP reports.
The measures came into force in July as ships were already at sea carrying hundreds of containers full of South African fruit to Europe, resulting in them being held up on arrival.
The Citrus Growers Association of SA has claimed the new measures were unnecessary as the country already has its own, more targeted way of preventing infestation.
"We had a fruitful meeting with the EU last Friday. We have managed to negotiate a settlement, which will see clearing all containers stuck in EU ports. So far we have cleared more than 300 of the 509 containers stuck in the EU," Reggie Ngcobo, spokesperson of the department, told Fin24 on Wednesday.
South Africa is the world's second largest exporter of fresh citrus after Spain, and citrus exports worth nearly R654 million were stuck in containers in EU ports. The SA government recently filed a complaint with the World Trade Organisation (WTO) after the EU introduced new plant and health safety requirements that local orange farmers said threaten their survival.
Europe is the largest market for South Africa's almost $2 billion citrus industry, accounting for 37% of all exports, according to the CGA. The CGA has confirmed that a new deal has been struck.
