The Economic and Financial Crimes Commission (EFCC) accused 11 defendants of "official corruption", according to court documents.
Shell, Eni and Agip, Eni's Nigerian subsidiary, are alleged to have corruptly given the "aggregate sum of $801 million" to Nigerian businessmen and politicians.
This is the latest probe into the controversial 2011 oil deal that highlights endemic corruption within the sector.
Italian prosecutors are also looking into the purchase of the OPL 245 block prospecting license.
OPL 245 is located in deep offshore waters in the Gulf of Guinea estimated to hold at least 9 billion barrels of crude reserves.
Oil majors Shell and Eni have both denied wrongdoing.
"Eni did not do anything wrong," said the chief executive of Eni Claudio Descalzi to the Financial Times in February.
"At every stage, we have acted in compliance with all applicable law?.?.?.?Eni and Shell paid the government of Nigeria, and were not involved with the government decision on how to use such money."
Nigerian President Muhammadu Buhari secured a historic first win for an opposition leader when he defeated Goodluck Jonathan in the 2015 presidential elections.
He campaigned on a platform to target rampant corruption and has said "mind-boggling" sums have been stolen from the public purse.
His government has arrested a series of high-ranking officials from Jonathan's administration on corruption charges but few have been convicted.