Multitalented artist Winnie Khumalo hopes her health will improve when she goes under the knife in J.
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]," she said.
"A helicopter flew overhead [and] did a rough estimate of the protesters. We can say that there were about 1,000 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."
Eyewitnesses at the scene said that there were nearly 3,000 people protesting.