"In 2009, 245,000 Zimbabweans applied for the permits. This year, 208,000 applied," department spokesman Mayihlome Tshwete told The Anadolu Agency on Friday.
He said there were many reasons why only 208,000 people applied for the special permits this year compared to the slightly higher number in 2009.
"Some might have gone back to Zimbabwe, got married or finished their studies here," the official, speaking by telephone, said.
Media reports had suggested earlier Friday that up to 40,000 Zimbabwean nationals could face deportation after failing to apply for the permit.
"In any country, a foreign national who lacks a permit faces deportation," Tshwete said, but denied reports that as many as 40,000 would be expelled from the country.
Zimbabweans living illegally in South Africa have – due to the difficult political and socio-economic conditions in their country – had the opportunity since 2009 to legalize their residency by obtaining special permits.
Last August, Home Affairs Minister Malusi Gigaba announced the launch of the Zimbabwean Special Permit (ZSP) of 2014, which allows holders to study, work and carry out commercial activities in the country until December 2017.
"I did not apply for the special permit because I use an asylum-seekers permit," Lovemore Ndebele, a Zimbabwean national living in Johannesburg, told AA.
Ndebele said that for years people had been given different types of permits.
"My cousin got a student permit and completed her studies. She has since returned home," he explained.
An estimated three million Zimbabwean nationals reside outside their country, with the majority in South Africa and Botswana and others in countries such as Britain, Canada and the United States.
The southern African country witnessed a mass exodus in 2008 amid economic turmoil and disputed elections, which led to the mistreatment of some opposition figures.
In a Wednesday statement, the Department of Home Affairs said that, as of Tuesday, as many as 207,802 applications had been received, while 198,840 appointments had been booked through the VFS system.
It also extended its gratitude to all the Zimbabweans who had taken part in the application process.
South Africa is home to thousands of refugees from Somalia, Ethiopia, Eritrea, Burundi and the Democratic Republic of Congo (DRC), among others.
The mineral-rich country has also attracted thousands of migrants from other continents.