Airlink is experiencing some delays and rerouting passengers on Thursday following the grounding of 14 aircraft due to safety concerns.
"We've obviously experienced some minor delays. All passengers are accommodated and will reach their destination," said Airlink spokesperson Karin Murray.
"We are using the existing fleet and also using additional rerouting on SAA and on other flights."
Fourteen of Airlink's Jetstream aircraft were grounded after the SA Civil Aviation Authority (SACAA) suspended their airworthiness status at midnight on Wednesday.
Murray said she could not give the exact number of passengers affected by the grounding on Thursday, but "a few hundred" had been part of the reshuffling.
"There will be some inconveniences," she added. "Until further notice, on a daily basis we have a plan."
Asked about the effect on public confidence in the airline, Murray said, "Obviously we are very concerned and we apologise in terms of the anxiety and inconvenience caused. Safety is our priority."
Murray said the airline would work to "restore the damage that has been done and restore confidence".
The manufacturer would now have to deal with the engine fault that was identified, said Murray.
"At this point in time the maintenance of the engine component is beyond Airlink's control. "They must move swiftly so normal operations can resume".
Meanwhile BAE Systems, the aircraft manufacturer, said in a statement it was sure that the grounded craft and its Honeywell-manufactured engine met international safety standards.
"BAE Systems remains confident that the Jetstream 41 and its Honeywell engine fully meets international regulatory safety standards." said BAE Systems Regional Aircraft spokesman David Dorman.
"We are in consultation with the SACAA and working with the engine manufacturer, Honeywell, to identify any appropriate controlling or corrective actions which will satisfy the SACAA concerns."
SACAA took the decision to ground the planes after a plane in the fleet had to abort a take-off in Nelspruit on Wednesday morning due to low oil pressure and smoke coming out of the left-hand engine.
"As a result of this second incident, which is similar in nature to the one that occurred in Durban in September 2009, resulting in one fatality, the SACAA resolved that the safety and airworthiness of the SA Airlink Jetstream aircraft fleet could no longer be guaranteed," SACAA said in a statement.
The near-accident happened in the midst of a CAA audit into the fleet following a number of accidents and near-accidents over the last three months.
The other aircraft types operated by SA Airlink ? the BAE 146 and Embraer 135 ? will continue to make their way into the sky.
Earlier, Transport Minister Sibusiso Ndebele said he would not stand for the loss of lives due to unsafe aircraft.
"As the department of transport, we will not stand guard at the gates of hell as a bonfire is brewed for the unnecessary sacrifice of our people," the minister said in a statement.
"This is our commitment to South Africa, this is our earthly covenant with all users of our airspace."
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