The presidency said on Thursday evening that Yusuf Magaji Bichi has taken over from Lawal Musa Daura as director-general of the Department of State Services.
Daura -- a key ally of President Muhammadu Buhari -- was dismissed after ordering what the government called the "unauthorised takeover" of the National Assembly in early August.
Vice-President Yemi Osinbajo said at the time the actions, which prevented lawmakers from entering parliament, were "a gross violation of constitutional order" and the rule of law.
The DSS under Daura was often accused of high-handedness and abuses against perceived political opponents of the Buhari administration.
The blockade came after the leader of the Senate, Bukola Saraki, defected to the main opposition from the ruling party.
Saraki, who has been at loggerheads with the executive since he took up the post in 2015, has since declared his intention to stand for president next year.
Buhari's office said the new spy chief was a "core secret service operative" who began his career with the Nigerian Security Organisation (NSO), the forerunner of the DSS.
Nigeria is facing multiple security threats, including from Boko Haram, where there is mounting concern about its IS-backed faction after a string of recent attacks on the military.
Security services are also stretched by a flare-up of violence in the long-running resources conflict between farmers and herders in central states.
There remain lingering threats to oil and gas infrastructure from militants in the southern Niger Delta region.