A public notice on Saturday said the exercise would take place between 9am and 11am.
The notice said the exercise might disrupt the free flow of traffic around the airport.
“The exercise entails armed troops descending from a helicopter flying at low level and movement within the terminal building,” the notice read.
“The exercise may also disrupt free flow of vehicular movement in and out of the airport. Members of the public, particularly air passengers are advised not to panic but go about their normal business.”
The Lagos airport is the busiest in West Africa.