President Jonathan's announcement of the audit addresses a crisis that has been simmering for several weeks
Lamido Sanusi, who was ousted by Jonathan as central bank governor last month, said the money came from sales made between January 2012 and July 2013 by the state-owned Nigeria National Petroleum Corporation (NNPC) that was not remitted to the treasury.
It is unclear whether the revenue, being generated at a rate of more than $1 billion a month, was still being diverted.
News of the audit came buried in a presidential statement attacking Lamido Sanusi. It insisted that his removal from his post as head of the central bank was not related to whistle blowing about what the statement termed "the phantom missing funds"
Jonathan also denied Sanusi's charges that the money has been diverted to fund campaigning for February 2015 elections.
The statement also refutes Sanusi's latest charges that the government was trying to bury the mystery of the missing petrodollars.
"In keeping with its avowed commitment to full transparency, openness and accountability in governmental affairs, the Federal Government has authorized the engagement of reputable international firms for the recommended forensic audit of the Nigerian National Petroleum Corporation accounts," it said.
Campaigning against corruption
Nigerians were largely skeptical. Olaonipekun Adeyemi is the founder of the Patriots for New Nigeria Initiative, an anti-corruption group. He told DW they were not going to "keep quiet" in spite of the investigation. They would be pressing ahead with a protest they were organizing. "We want to know the true situation with the twenty billion dollars missing money, what is happening." he said.
Another Nigerian, Abiodun Ayodele told DW in Lagos "It was a good thing that the president had already set up a probe." But Ayodele also thought the government "will start something they will not be able to finish and at the end of the day everything will be swept under carpet."
When he was re-elected in 2011, Jonathan promised to fight corruption that keeps an elite fabulously wealthy while the majority of Africa's most populous nation of some 170 million people struggle to survive on less than $1 a day, according to U.N. statistics.
But now Jonathan's administration is seen as shielding the corrupt, most infamously by the pardon issued by the president last year of the ex-governor from his home state of Bayelsa, Diepreye Alamieyeseigha, because he was "remorseful" after being convicted of money-laundering.
Alamieyeseigha's properties and funds in the United States and Britain were seized as proceeds of corruption in recent years, and he had jumped bail from Britain in 2005.
Previous investigations of billions in missing public funds have ended without resolution, with no one held to account and no money recovered.
No one has been prosecuted for a fuel subsidy scam uncovered in 2012, in which some $17 billion was paid to companies for fuel that never was delivered.
DW correspondent Sam Olukoya said Nigerians were getting increasingly frustrated about frequent reports of "public officers stealing huge sums of state funds."