Authorities said on Friday that a boy, 14, had been arrested for spying on security procedures at Abuja's airport.
Security forces are working to prevent "any possible attack and to ensure adequate security at the airports" in response, the agency said.
It said agents are still searching for militants who were directing the boy.
He was instructed to pass on details about "passenger screening, boarding procedures and other processes in the departure and arrival halls," according to a statement from the Department of State Services (DSS).
The DSS said the arrest of the 14-year-old had "disrupted a spying network mounted by the Boko Haram terrorists".
It said the network was discovered on Monday and it was working with aviation authorities to pre-empt any attack at the Nnamdi Azikiwe International Airport.
Boko Haram has waged a six-year violent campaign in Nigeria, killing thousands and forcing millions to flee their homes.
The bloodshed has been largely confined to the northeast of the country where the group has declared an Islamic state.
Why Boko Haram remains a threat
Nigeria's intelligence agency has warned of a possible attack on the airport in its capital after disrupting what it said was a Boko Haram cell.