He told the BBC Newsday programme that the continent was now reporting about 30,000 new cases daily compared to 18,000 in mid-July.
The health agency's tally shows that Africa has so far confirmed nearly 3 million coronavirus cases, with 68,755 deaths.
Countries like Rwanda, Namibia, Zimbabwe and the Democratic Republic of Congo have imposed new restrictions to limit the virus' spread.
Dr Nkengasong said that face masks were the continent's best hope to prevent the spread of the virus and he urged governments to subsidise them.
He added:As you move across the continent it is unfortunate that you see many citizens are not wearing [face] masks consistently or not wearing them at all, and you see very limited social distancing. I think this is serious, the second wave is extremely aggressive."