The already endangered African penguin is being driven away from its natural habitat off the east coast of South Africa due to noise from ship refuelling, a scientific study has found.

The number of African penguins on St Croix island in Algoa Bay, once the world's largest breeding colony of the birds, has plummeted since South Africa started to allow ships in the area to refuel at sea, a process known as bunkering, six years ago, the study found.

Situated in a busy shipping lane along South Africa's east coast, Algoa Bay is rich in marine and bird life where southern right whales roam in its sheltered waters.

"We found the noise levels, which were already high, to have doubled," since bunkering began, Lorien Pichegru, acting director of the Coastal and Marine Research Institute at Nelson Mandela University, which led the study, told Reuters on Tuesday.

Elevated noise levels affect marine animals' ability to find and corral prey, communicate or navigate properly, scientists have previously found.

"This year we are at 1,200 breeding pairs at St Croix from 8,500 pairs in 2016, an almost 85% decrease since bunkering started in South Africa," Pichegru said. "I was counting the dead birds every month on the beach of the bay."

The new study, published on Aug. 10 in the peer-reviewed 'Science of the Total Environment' journal, is the first to explore the impact of maritime traffic noise pollution on a seabird, and the consequence of offshore bunkering activities on underwater noise levels, researchers said.

South Africa's Maritime Safety Authority (SAMSA) in 2016 awarded the country's first offshore bunkering operator's license to Aegean Marine in a controversial closed tender, and then awarded two subsequent licenses to SA Marine Fuels and Heron Marine in 2018 and 2019 respectively.

Aegean, now trading as Minerva, is a wholly-owned unit of global energy trader Mercuria and Heron Marine is a subsidiary of rival Trafigura, while SA Marine Fuels is majority owned by Oryx Energies.

Trafigura, Minerva and Oryx Energies did not immediately respond to requests for comment.

A moratorium on new licenses, in place since August 2019, will only be lifted once an environmental impact assessment is completed by port authorities. The assessment is expected next year, a SAMSA official said.

Nelson Mandela University's study used vessel-identification tool data to estimate underwater noise from ships as a proxy for underwater ambient noise in the area.

In 2019 oiled penguins were found in Algoa Bay after an oil spill from ship-to-ship bunkering and conservationists have called for bunkering to be banned in the bay.

Pichegru said penguins in the St Croix islands were already struggling to breed due to a variety of challenges, including industrial fishing of scarce prey.

"Bunkering did not kill all the penguins, it was just the thing that made the whole ecology tip over and then the penguins couldn't cope with that," she said.