The audit, ordered last week by a Senate committee investigating allegations of corruption in the oil industry of Africa's second largest economy, could become political dynamite as Nigeria heads into a presidential election in 2015.
Nigeria, Africa's most populous nation and one of its leading oil producers, is considered one of the most corrupt states on the continent, with much of the graft centered on the oil industry, whose revenues provide around 80 percent of the state budget and more than 90 percent of export earnings.
The West African country's "oil and gas industry has proved remarkably resistant to reform because it's so intertwined with the interests of political elites," Joshua Holland, African analyst with PFC Energy in Washington, told the Financial Times.
"While Nigeria has been running in place, other countries have been surging ahead and the industry has followed."
Central Bank Gov. Lamido Sanusi blew the whistle in a letter to President Goodluck Jonathan in September 2013 claiming the Nigerian National Petroleum Corp. failed between January 2012 and July 2013 to account for 76 percent of the revenue from crude oil sales that should have been deposited in state coffers.
According to his figures, the government is being short-changed by up to $1 billion a month.
On top of this, Sanusi questioned why the NNPC was still financing fuel subsidies eliminated by a presidential directive in 2009 and why $20 billion in state subsidies was not remitted by the corporation in 2012-13.
All told, that adds up to $50 billion, and does not include the loss of an estimated 150,000 barrels of crude that's being stolen every day by armed militias or crime syndicates, often indistinguishable, in the oil-rich Niger Delta of southern Nigeria.
A 2013 report by the Royal Institute of International Affairs, a London think tank, said this trade is worth between $3 billion and $5 billion a year.
Sanusi has battled to maintain his independence from government since his appointment in June 2009. That includes tackling major financial fraud during a 2009 banking crash.
His oil industry allegations have a raised a political storm and he's come under growing political pressure from critics inside and outside the government who accuse him of politicizing the issue.
Large revenue shortfalls in what the Financial Times calls "Nigeria's notoriously opaque oil industry" have been periodically exposed over the years, but the vast sums allegedly involved in the current scandal dwarf all earlier controversies.
Jonathan's office did not announce Sanusi's allegations at the time, but Sanusi's letter leaked out in December. In January, Jonathan demanded Sanusi's resignation. He refused and said he will see out his term which ends in June. He can only be forced out before then by the senate.
"We believe we should have an independent forensic audit of these accounts," declared Finance and Economy Minister Ngozi Okonjo-Iweala.
"It's the only way Nigerians will be satisfied that a proper accounting is being done," she said.
The NNPC said Sanusi's numbers revealed a "gross misunderstanding" of how Nigeria's state's oil revenues accrue.
A senior official said about $24 billion could be accounted for in oil swaps, in which crude oil is exchanged directly for refined products with no cash involved. Another $16 billion in taxes and royalties to international oil companies under production- sharing contracts would be paid into separate accounts.
But the Financial Times reported that independent analysts have so far identified shortfalls of $15 billion in NNPC figures.
This has resulted in a sharp drop in foreign investment in Nigeria's increasingly trouble oil industry.
Along with the actual theft of oil on an industrial scale in the Niger Delta, Jonathan's home region, this loss of confidence has slashed Nigeria's oil production to below 2 million barrels per day, threatening its status as Africa's largest exporter.
Oil majors are increasingly moving offshore. But they have drilled only five deepwater wells in the last three years, while Angola and Ghana have drilled 25 apiece, according to the Wood McKenzie energy consultancy of Edinburgh.