Lawal Daura, director-general of the Department of State Services (DSS), has been arrested.
He was arrested after Acting President Yemi Osinbajo relieved him of his duties on Tuesday afternoon.
Osinbajo had summoned Daura alongside Ibrahim Idris, inspector-general of police, over the siege laid to the national assembly earlier in the day.
Federal lawmakers were denied access to the legislative chamber, fuelling speculations that the ruling All Progressives Congress (APC) was perfecting its plot to oust Senate President Bukola Saraki.
The two security chiefs arrived Aso Rock at different times. While Idris got to the presidential villa at 12;35pm, Daura got there at 1:15pm.
After briefing Osinbajo, the former DSS DG was whisked away.
State house correspondents who were waiting to speak with the security chiefs did not know that Daura had been taken away through another exit.
Osinbajo had condemned the invasion, distancing the federal government from it.