Police were called in to curb a violent protest at the Tshwane interim refugee reception office in Pretoria on Wednesday, the home affairs department said.

Spokesman Ronnie Mamoepa said the dissent disrupted traffic and business in the area and a number of vehicles were "pelted with stones".

He said the protests were sparked by Ethiopian nationals who "allegedly did not want to queue for services".

"A decision was made to suspend operations at the centre for the day, while serving women, children and the most vulnerable only."

Mamoepa said Home Affairs Deputy Minister Fatima Chohan would meet senior officials in the department to discuss Wednesday's events.

About 1000 refugees protested at the facility on Wednesday morning.

Police spokeswoman Captain Louise Reed said the refugees were unhappy with the way they were being treated at the offices and began to get "rowdy".

"They burnt a few tyres, but that was it. Some of them are still hanging around and seem to be negotiating with the head people [at the office]. A helicopter flew overhead [and] did a rough estimate of the protesters. We can say that there were about 1000 people there, but it's all over now, and to my knowledge no one was injured."

Legal organisation Lawyers for Human Rights said the protest started just after 6am, when officials at the office allegedly refused to serve the refugees.

"The protest appears to be motivated by the poor access to the facility and the inability of asylum seekers and refugees to be able to get the services which are supposed to be provided by that office," it said.

"They will need to return next week if their permits are not renewed today, which will place many of them in a serious situation, where they will be vulnerable to arrest and detention if their permits lapse."

Witnesses at the scene said there were about 3000 protesters.