Home affairs department provincial head Yusuf Simons said the manager in question at the Customs House refugee centre was being investigated, the Cape Argus reported on Friday.
He said a home affairs supervisor allegedly saw the security official in question taking a bribe.
Many refugees reportedly complained that guards were demanding cash in return for helping them make progress in the queue.
The newspaper previously reported that many were forced to sleep outside the building to have a chance of getting to the front of the queue.
Some refugees said they had to camp on the pavement for up to four days in order to renew their asylum permits.
Violent clashes last month between guards and refugees lead to the police firing rubber bullets on them.
Simons said the centre was in the process of making new arrangements for refugees applying for extensions and appointed more staff.
"We decided last week that instead of just extending asylum seeker permits, we also want to start finalising cases sooner," Simons told the newspaper. "We have scheduled more interviews with asylum seekers as a result."