Spokesperson Bayanda Mzoneli said the minister "just came to make sure the implementation of the amnesty for Zimbabwean nationals with fraudulent documents was going well".
On Tuesday, a woman collapsed when Zimbabwean nationals lining up to claim amnesty at the regional office were sprayed with a substance by a police officer.
This happened around 3pm when disorder broke out among the several hundred Zimbabwean nationals queuing at the office in Harrison Street in the Johannesburg CBD.
Mzoneli said police were forced to intervene after there was a "misunderstanding" between amnesty seekers.
The misunderstanding arose after a group of Zimbabwean nationals decided to camp outside the office on Sunday to get a head start for applications on Monday.
But police asked them to leave after writing their names on a list.
The list was given to home affairs officials on Monday morning.
"Since Monday, we've had to process the list of people from Sunday and also the people who come every day... there was a misunderstanding yesterday [Tuesday] between the people who were listed on Sunday and the people who arrived at the office on Tuesday," said Mzoneli.
"It got sort of out of hand and we had to request assistance from the police."
The office can process 135 applications a day -- excluding enquiries -- and 359 people's names appeared on the Sunday list, he said.
Mzoneli said the applications of those from the Sunday list had been processed by Wednesday.
"The Sunday people are done."
He said the deputy minister also visited the Bloemfontein office on Wednesday morning.
"The deputy minister has observed that the Bloemfontein office receives fewer numbers... so perhaps the deployment of officials should match the demand of the office.
"So we might move officials from one office to the next."
A final decision would only be made after an audit had been done of all the busy and less busy home affairs offices, Mzoneli said.
On Wednesday morning, a group of people were waiting patiently outside the Harrison Street office, some saying they had been queuing since 4.30am. The situation was calm.