The five men charged allegedly persuaded a senior bank official at Banco Noroeste in Sao Paolo to send the money for construction of an airport, promising him a $10 million kickback.
But Monday, Abuja High Judge Lawal Gumi decided since the crimes had not taken place in the Nigerian capital, but rather Lagos, he had no jurisdiction to try the case.
Tuesday, it was still unclear if a court in Lagos would hear the case.
Nuhu Ribadu, head of Nigeria's Economic and Financial Crimes Commission, said the swindle took place over a four-year period starting in 1995.
The discovery of the scam has led to criminal investigations in Switzerland, Britain, the United States and Brazil, said Ribadu.