The fire on Wednesday night started as people in the city were trying
to cope with two days of heavy rain, which has left many homeless and
without power.
The flooding hampered rescue efforts and may have led to the fire, the BBC's Sammy Darko reports from Accra.
President John Dramani Mahama has announced three days of national mourning to begin on Monday.
It
is thought that people were in the petrol station sheltering from the
downpours when the fire broke out, our correspondent says.
President Mahama visited the burnt-out petrol station and described the deaths as "catastrophic" and "almost unprecedented".
He vowed to take tough measures to stop people building on waterways, which appeared to have been a factor in the disaster.
"I
think that the time has come for us to remove houses out of water and
the public should understand that it is necessary to save everybody
else," he said.
Following an emergency meeting of cabinet and
security chiefs on how to tackle flooding, the government says it will
release £9m ($14m) to help flood victims.
Schools were closed across the capital and children asked to stay at home.
Bus conductor Yaw Aforve was sleeping in his vehicle which was parked at the petrol station when the fire started.
He said he jumped into the floodwaters and when he came up for air, the fire burnt his face.
"I was swept away by the water to the other side [of the road]," he added. "I saw so many people screaming and shouting."
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