The president also expressed concern about the absence of a national carrier and directed the ministry to look into the possibility of having one as soon as possible.
The permanent secretary later told State House journalists that Buhari ordered her ministry to begin the process of securing the management of the Nigerian airspace which, she noted, Ghana had been managing since 1945.
The permanent secretary hinted that Togo and Benin Republic had equally concluded arrangements to take over their airspaces from Ghana.
"We've a directive by the president to start the process of securing the management of the Nigerian airspace over the Gulf of Guinea which Ghana has been maintaining since 1945, and there is a move on the ground by Togo and Republic of Benin to take over their own airspace from Ghana," she said.
Bello said the president also ordered the ministry to expedite action on the establishment of a new national airline for the country.
According to the permanent secretary, the president is worried that Nigeria does not have a national air carrier.
She said Buhari was told that domestic airlines were hugely indebted to regulatory agencies under despite the federal government's N300 billion intervention fund designed to boost their operations.
The permanent secretary expressed hope that the four state-of-the-art airport terminals being constructed with Chinese Bank loan would be ready by first quarter of next year.
Presidential spokesperson Femi Adesina later in a statement quoted Buhari as expressing concern about the enormous debt profile of the nation's aviation sector.
The president was also quoted as assuring that his government would act quickly to redress the situation.