Mpofu said stakeholders met on Monday to develop a plan to ensure supply.
She said the supply of fuel was "stable" at the airport but demand often outstrips supply, mainly because of the non-availability of the Transnet line.
She said the airport now had jet fuel stock of 3.5 days.
"It's comfortable for us to be at 3.5 days but we've indicated that we've had supply challenges," Mpofu said.
Mpofu said a consignment of jet fuel has arrived at Durban harbour and was being pumped into a refinery at the National Petroleum Refinery which will help alleviate the problem at OR Tambo.
Siganeko Magafela, head of security of supply at the SA Petroleum Industry Association, said they expected the fuel in Durban to arrive at the airport on May 19.
"We expect the shipment to alleviate some of the issues and we are confident we will be able to meet this challenge," Magefela said.
Tshepo Mokoka, CEO of the Central Energy Fund, said they would deal with any shortages by making available an emergency supply in partnership with the private sector.
George Mothema, CEO of the Board of Airline Representatives of South Africa (Barsa), said they were pleased with the CEF coming on board and helping their members affected by the supply challenges.
"This should in the short-term address the issues of tankering and the cancellation of flights," Mothema said.
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