South Africa's image has been harmed internationally by the Khalid Mahmood Rashid case, Deputy Foreign Affairs Minister Aziz Pahad said on Tuesday.
He said there has been a lot of publicity locally and internationally about the case and many people now believed South Africa was among countries which endorsed extraordinary rendition of people.
"We want to deny that," Pahad said.
Although his department was not involved in the Rashid case it would have to see how it could "minimise" the "negative messages".
"It's a matter that government is concerned with and we would try to resolve it as quickly as we can," Pahad said.
This comes after Rashid's lawyer Zehir Omar on Monday asked the International Criminal Court to investigate his client's disappearance from South Africa.
Rashid disappeared at the end of last year from Estcourt where he was picked up in a night raid on his home for being an illegal immigrant.
His arrest was contested in court but Home Affairs officials said Rashid was deported to Pakistan within days after his arrest.
There were, however, fears in the Muslim community that Rashid may have been taken to an international detention centre. - Sapa