Importers are accused of withholding petrol because of a payment dispute with the government, which they deny.
This is the biggest fuel shortage in Nigeria since President Muhammadu Buhari took office in May.
Nigeria is Africa’s main oil exporter but imports most of its petrol because it lacks the capacity to refine it.
The fuel is imported at a subsidised price under a scheme operated by the state-owned Nigerian National Petroleum Corporation (NNPC).
Earlier this month, the government approved the payment of $2.1bn (£1.4bn) to the importers, or wholesale fuel sellers, to settle subsidy claims.
However, payment has been delayed because parliament has not yet approved it.
The BBC’s Bashir Sa’ad Abdullahi in the capital, Abuja, says previous governments tended to pay the wholesale fuel sellers without parliamentary approval.
But it seems that President Buhari is trying to stick to the law by refusing to release such a large sum of money without parliamentary scrutiny, he says.
Mr Buhari took office partly on a pledge to curb corruption in the oil sector.
One motorist in the main northern city, Kano, told the BBC Hausa Service that he spent the night in his car while waiting in a queue to fill petrol.
“I have been here for more than 12 hours and I don’t know if I will get the fuel at all,” he said.
Another motorist said he was in the queue for about eight hours and “only people with connections were being allowed to buy the fuel”.
The fuel subsidy scheme has become an enormous scam, our correspondent says.
The wholesalers often pretend to bring in a lot more oil than they do and pocket the money they get for the petrol that is not delivered, he says.
In May, the country was brought to a standstill when the importers went on strike following a row over payments with the outgoing government of President Goodluck Jonathan.