NNPC earned $65.3 billion from crude oil sales between January 2012 and July 2013 but only remitted 24 percent of this to the government's account and $49.8 billion was still outstanding, according to a letter from the CBN Governor Lamido Sanusi to President Goodluck Jonathan.
NNPC sold 46 percent of Nigeria's oil in the 18-month period but its remittance amounted to only one-third of the taxes paid by private oil companies, like Royal Dutch Shell and Exxon Mobil, which exported the other 54 percent, the letter claimed.
NNPC says the CBN has misunderstood the figures and denies such claim.
"The matter will be investigated by the Senate finance committee headed by Ahmed Markafi and (it is) to report back as quickly as possible but certainly not more than one week," Senate President David Mark said.
NNPC has been criticised for lacking transparency and for diverting funds in several investigations in recent years but the central bank governor appears to be one of the most high-profile figures to have brought up the issue with Jonathan.
OPEC-member Nigeria is Africa's second largest economy and top oil producer, pumping around 2-2.5 million barrels per day. Oil revenues make up 80 percent of government revenues.