The SAHRC has launched another investigation into reports of an alleged protest which was staged by refugees at the Lindela Repatriation Centre on Monday.
It was reported that the refugees were protesting against an unlawful practice by the department, which had allowed them to be held captive for longer periods.
However, the department had denied the allegations that there was a riot.
According to the Immigration Act, the department cannot detain refugees for more than 120 days.
SAHRC spokesman Vincent Moaga said the commission had decided to launch an investigation following a visit by their monitoring team to the centre on Tuesday.
Moaga confirmed that the commission was also investigating an earlier complaint relating to alleged appalling conditions and treatment of refugees and asylum seekers at the facility from a consortium of eight NGOs, who worked closely with refugees and asylum seekers.
He added these violations were of concern as it appeared to be becoming endemic and systemic.