The Nigerian National Petroleum Corporation (NNPC) provided no explanation for the missing funds, the auditor general told MPs.
Oil revenue accounts for two-thirds of the government's funding.
President Muhammadu Buhari has promised to crack down on corruption since coming to office last May.
The NNPC has not commented on the auditor general's findings.
This finding by the auditor general, while shocking, is not a surprise.
Officials from the previous administration allegedly indulged in wholesale corruption where billions of dollars of oil funds simply disappeared.
When the then central bank governor Lamido Sanusi pointed out that billions of dollars were missing from the treasury, he was sacked from his job.
Nigeria's oil reserves should have been blessing for Nigeria to be used to build infrastructure and invest in social services.
Instead, it has been a curse, a lubricant that has produced massive corruption and dysfunctional governments.
President Buhari was elected on a platform of cleaning up the country's notoriously corrupt politics.
But some officials from the previous administration accuse him of using corruption to pursue a political vendetta.
The state oil giant has been mired in corruption allegations and losing money for many years.
Last month, the government announced that the NNPC would be broken up into seven different companies.
A separate audit ordered under former President Goodluck Jonathan and carried out by global accountancy firm PwC, found that the NNPC had failed to pay the government $1.48bn between January 2012 and July 2013.
It did not provide a total figure for how much revenue the NNPC should legally have handed over to the treasury.
However, the company said that it could not vouch for the integrity of the information it was given when it conducted the audit.
Nigeria is Africa's biggest oil producer, but the economy has suffered because of the recent decline in the price of oil.

The Tykes announced they had agreed a move for the 22-year-old a week ago, after the batsman told Worcestershire he wanted to leave at the end of the season when his contract expired.
Kohler-Cadmore averages 48.40 in the County Championship so far this summer.
He is now available for Yorkshire with immediate effect.
"Obviously it was a massive decision to move home and I find it incredibly exciting," Kohler-Cadmore told Yorkshire's club website.
"I'm really looking forward to getting stuck in and part of my decision to move was to challenge and test myself in what is a great environment and a very strong squad. Hopefully this will help me improve and push me on to higher levels."
In a statement Worcestershire chief executive Tom Scott said: "Worcestershire County Cricket Club have mutually agreed with Tom Kohler-Cadmore and his representative of the immediate release from his contract with the club.
"We would like to thank Tom for the contribution he has made at New Road and wish him continued success in the future."
Kohler-Cadmore, who was dropped for Worcestershire's last Championship match against Sussex after saying he wanted to leave New Road, impressed the Tykes first hand in May.
He hit five sixes and 10 fours in his match-winning 118 against Yorkshire at New Road to help propel Worcestershire into the One-Day Cup semi-finals.
Kohler-Cadmore also caught the eye in May last year when he hit the fastest century of the 2016 season - a stunning 127 off 43 balls against Durham in the T20 Blast at New Road, breaking Graeme Hick's 12-year-old record T20 score for the county.
He came through the junior system at Yorkshire before going to boarding school in Worcestershire at Malvern College.
Under the terms of the deal, Kohler-Cadmore will not be eligible to play against Worcestershire in 2017, meaning he will not face them in the One-Day Cup semi-final should Yorkshire beat Surrey in their quarter-final on 13 June.
Nigeria's state-owned oil company has failed to pay the government $16bn (Â£11bn) in a suspected fraud, according to an official audit.
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Yorkshire have confirmed the signing of Tom Kohler-Cadmore on a three-year deal after he was released from his contract by Worcestershire.