The Civil Aviation Authority has downgraded the Mthatha airport from Friday, January 25.
According to a release by South African Express, the downgrade follows "a negative audit finding" against the airport.
South African Express(SAX) advised customers that the airline offered flight cancellations between Johannesburg and Mthatha.
"We are working jointly with the Eastern Cape provincial government authorities to find a speedy solution so that operations at the airport can resume. We apologise to our passengers and customers for the inconvenience caused by these cancellations, which are outside of our control," the statement read.
Affected customers are requested to call SA Express Customer Care on 011 978 2355. All booked passengers for the period will be fully refunded.
Meanwhile, earlier this month, SAX announced it will resume flights from Cape Town base to Bloemfontein and Walvis Bay in Namibia as it continues to accelerate the phased-in restoration of its network.
The once-daily service between Cape Town and Walvis Bay will resume on Saturday. SAX also said that it will operate daily flights between Cape Town and Bloemfontein with effect from Sunday, with two frequencies from Monday to Friday, and one flight on Saturdays and Sundays.