The Home Affairs Department is confident it will hand over all Zimbabwean Exemption Permits by the end of November.
The permits allow Zimbabweans to work, study or conduct business in South Africa.
Over a 180, 000 applications were received.
The Department says about 2, 000 applications have not been completed because of expired passports.
Those affected have been given until the 15 December to submit new travel documents.
Home Affairs said it is still struggling to get hold of 84 people to have their fingerprints retaken.