He said a false notification was activated about flight SA 417, which left Johannesburg at 13:05 and landed in Port Elizabeth at 14:30.
"The plane was already airborne when we came to know of the notification," Tlali said.
Emergency services and extra security were sent to the Port Elizabeth airport to meet the flight when it landed.
Tlali said the plane, with its passengers still on board, was inspected and declared safe and incident free.
"Neither passengers nor crew [cabin and flight deck] were harmed as there was no hijack incident at all."
He said it was not known whether the SA Civil Aviation Authority (CAA) would investigate.
"I cannot speculate about the facts, but we remain concerned and are very keen to find out the origins of this incident. Incidents of this nature impact on... operations in many ways," he said.