"The first (step) is the recovery of the 382 billion naira," AIG Imokhuede, the head of the committee told reporters at the presidential villa after submitting the report to Jonathan.
"The next is possible criminal investigation and prosecution of the OMT (oil marketing and trading companies) ... also, the external auditors and any government functionaries who served will be further interviewed to determine the roles if any in the issues that were discussed."
Imokhuede did not name specific companies but some of the world's largest oil traders import petrol into Africa's most populous nation, along with marketers owned by some of the richest and most powerful Nigerians.
Nigeria is among the top 10 crude oil exporters in the world but due to decades of corruption and mismanagement it has to import most of its refined fuel needs.
Nigeria scrapped subsidies on gasoline imports on Jan. 1, potentially saving the country over $6 billion. But more than a week of strikes and protests erupted across the country against the higher cost of motor fuel, forcing the government to partially reinstate them.
Nigerian legislator Farouk Lawan led a parliamentary probe into the subsidy earlier this year, uncovering $6.8 billion in fraudulent payments over three years.
RISK OF SHORTAGE
But now his committee's report is being called into question over allegations Lawan demanded, and took part of, a $3 million bribe from one of Nigeria's richest oil tycoons to remove him from the list of fraudsters.
Lawan's lawyer said he took $500,000 offered by the tycoon, but only in order to expose him, saying he disclosed it to parliament and left the cash with parliament.
Lawan's report not only highlighted the fuel traders crimes but also pointed the finger at high level politicians, including Oil Minister Diezani Alison-Madueke. Jonathan's probe has focused on oil companies rather than government officials.
The Finance Ministry has held off subsidy payments until probes into marketers have been completed, prompting anger from importers and risking fuel shortages.
People queued for petrol at inflated prices in Nigeria's oil-producing Niger Delta on Tuesday. Nationwide fuel shortages and a spike in prices risks further public unrest.
Fuel union Jetty and Petroleum Tank Farm Owners of Nigeria (JEPTFON) is shutting down fuel distribution facilities this week and another labour group, the Depot and Petroleum Marketers Association (DAPPMA), threatened to join them within 48 hours if government did not pay outstanding subsidies.
The subsidy is stretching Nigeria's finances and draining oil savings. The minister of state for finance said in June Nigeria only had 370 billion naira ($2.29 billion) left to pay subsidies, out of the 888 billion in the 2012 budget.
The central bank has said the subsidy budget will run out well before the end of the year, which means they will need to raid savings to pay for it. Powerful state governors have said they will take the federal government to court for what they call "illegal" over-budget subsidy payments.