Of the 180,000 applications, 108,485 permits were processed and had been collected, said Makgola.
Meanwhile, 39,089 were in the process of being collected or sent to the various collection offices, he added.
The department has urged 1,932 applicants who had expired passports to contact the Zimbabwean consulate, as their application could not be processed.
While this may be a relief for many, it still denies Zimbabweans permanent residency in South Africa.
The department said it had met with the Zimbabwean Consulate which had undertaken to expedite the passport applications of those who did apply.
The ZEP came into effect in January 2018, and it will expire in December 2021.