The commission received eight complaints, including two from children, against the department of home affairs, said SAHRC spokesman Isaac Mangena in a statement.
The asylum seekers claimed there were new asylum applicants who had been trying to legalise their status with the department in Cape Town to no avail.
They claim the applicants resorted to sleeping outside the reception centre in order to make it into the building to process their documents.
They complained of being thrown out of the reception centre by security guards there and that they were told by the reception centre's officials to go to other provinces to have their applications processed.
"The home affairs officials argue that capacity is the problem, but based on our discussions with them today, this is not the issue," said Mangena.
The investigation was in line with a decision by the High Court in the Western Cape, instructing the minister of home affairs to ensure that the refugee reception office in Cape Town should remain open and functional to allow asylum seekers an opportunity to make their applications and be issued with Section 22 permits.
Mangena said the commission would engage with the department as well as civil society groups concerned.
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