Nigeria spent N1.274 trillion, about $3 billion on fuel subsidies in the first five months of this year, a document sent by the NNPC to the government showed.
The NNPC document, according to a Reuters report, showed that the corporation has not remitted any revenue from its oil and gas activities to the Nigerian government between January and May this year.
Nigeria exports crude oil and imports refined petrol, suffering intermittent fuel shortages.
The subsidy has seen the country raise its deficit forecast twice this year and increased borrowings to cover the cost.
Petrol prices in Nigeria are among the lowest in the world as the government pays to keep pump prices fixed despite rising global oil prices.
A plan to abolish the subsidy was scrapped until after national elections in February 2023 and $9.6 billion was added to planned spending to cover it, putting pressure on the budget.
Nigeria faces double-digit inflation and low growth, amid a shrinking labour market and mounting insecurity.
Finance Minister Zainab Ahmed said last month that the country was barely able to cover the cost of imported petrol from its oil and gas revenue.