Amani Abou-Zeid told a news conference that due to the prolonged lockdown and border closures to curb the spread of the virus, the air industry will be greatly impacted.
"Some airlines in the continent will not make it post-COVID-19," she said.
"In Africa tourism is not luxury," she said. "This is our livelihood."
Despite a steady rise in coronavirus cases, countries across Africa are forging ahead with plans to resume air traffic.
A handful of states reopened their borders last week, including Zambia and Sierra Leone. Senegal has announced the resumption of international air travel from July 15.
"As we are going to open... we are also now pushing for intra-African tourism," Abou-Zeid said, calling for lower taxes, reduced ticket fees and visa facilitation to encourage "Africans to see Africa."
She hoped the reopening of the skies would "cushion some of the serious impacts on ...air transport and tourism."