In a statement seen on Friday by Reuters, Dangote Group said the cargo of 1 million barrels of Agbami crude it had purchased was the first of 6 million barrels that would enable an initial run of the refinery.
That will kick-start output of diesel, aviation fuel and liquefied petroleum gas, before the refinery later starts producing premium motor spirit, or gasoline.
Once fully running, the 650,000 barrel-per-day refinery funded by African billionaire, Aliko Dangote will turn oil powerhouse Nigeria into a net exporter of fuels, a long-sought goal for the OPEC member, which is almost totally reliant on imported fuels.
A Dangote Group spokesperson said the oil was expected to arrive at the refinery later on Friday.
The next four cargoes will be supplied by state oil company Nigerian National Petroleum Corporation in two to three weeks and a final shipment will come from ExxonMobil, Dangote Group's statement said.
Despite being Africa's biggest oil producer, Nigeria experiences repeated fuel shortages.
The West African nation spent $23.3 billion last year on petroleum product imports and consumes around 33 million liters of petrol a day.
"Our focus over the coming months is to ramp up the refinery to its full capacity," Dangote was quoted as saying in the statement.
Nigeria commissioned the refinery in May, after it ran years behind schedule. At a cost of $19 billion, the massive petrochemical complex is one of Nigeria's single largest investments.