Cairo is already on edge ahead of mass anti-government protests planned for June 30.
The government has blamed the latest crisis on rumours of shortages and black-market speculation.
Egypt has been plagued by fuel crises over the last year, promoting citizens to question the ability of President Mohamed Morsi and his government to run the country.
"Since the morning I have been going to one petrol station after another," said one man. "This is unfair, what should we do, where should we go?"
The crisis has also fed fears that the government is trying to foil protests planned by the opposition.
"It looks like the regime is falling and it is putting pressure on the people through shortage of subsidised goods like petrol," said one man as he waited to fill up his car.
The fuel shortage comes just a few days before the planned mass protest against Morsi's regime. June 30 marks one year since Morsi took office.
"Anyone who doesn't join the protests on the 30th deserves whatever they get for the next one hundred years," said another man waiting to get petrol on Tuesday.
Opponents charge that Morsi is monopolising power for his Muslim Brotherhood, excluding others, while failing to make progress towards solving the country's critical problems, like economic malaise, fuel shortages, electricity blackouts and increasing unemployment.
They demand that he step down and hold early presidential elections.