The defence chief, head of the army, navy and the air force were all retired and replaced with new officers.
An official statement on Monday said Mr Tinubu had “approved the immediate retirement of all service chiefs and the inspector-general of police, advisers, comptroller-general of customs from service … with immediate effect”.
Mr Tinubu has also dissolved the boards of all federal government institutions – but excluding some such as the judicial council, the electoral body and the police service commission.
The security changes come two weeks after he met security chiefs and ordered them to work jointly to tackle the challenges of terrorism, insurgency, banditry, oil theft and piracy.
Nigeria has been grappling with a rising wave of attacks blamed on jihadist groups and other criminal gangs, including bandits who mainly engage in kidnapping for ransom.
There were persistent calls by civil society groups during the last government for the security chiefs to be changed because of their inability to tackle the situation.