Emefiele was detained by a state security agency on June 10, a day after new President Bola Tinubu suspended him. A judge this month ordered the agency to file charges or release him.
Emefiele pleaded not guilty to two counts of illegal possession of a firearm and ammunition, Channels TV reported.
He has challenged his detention and has filed an application for bail.
Government lawyers had asked the courts in June to authorise Emefiele's detention for allegedly misappropriating funds and "criminal breach of trust", charges that carry lengthy jail terms if proved.
They secured a court order to hold Emefiele pending further investigations.
Emefiele was known for using unorthodox policies to keep the country's naira currency artificially strong and lending directly to businesses to try to boost growth.
Tinubu, who is embarking on the boldest reforms in Africa's biggest economy in more than a decade, criticised the central bank's policies under Emefiele at his inauguration in May, saying they needed "thorough house-cleaning", without providing details.
The central bank is due later on Tuesday to announce its first interest rate decision since Emefiele's suspension. One of Emefiele's deputies, Folashodun Shonubi, is acting central bank governor.
(Reporting by Chijioke OhuochaEditing by Alexander Winning and Nick Macfie)
Bola Tinubu, President of Nigeria, arrives for the closing session of the New Global Financial Pact Summit, Paris, France, 23 June 2023. The two-day summit aimed at seeking better responses to tackle poverty and climate change issues by reshaping the global financial system. EPA-EFE/Lewis Joly / POOL MAXPPP OUT