The explosion occurred as hundreds huddled under the cover of the gas station and nearby shops to stay dry.
Victims included drivers of public transportation and their passengers waiting out the rain away from the open terminal where buses operate from, authorities said.
Others were motorists who had stopped to refuel, but they perished instead, said Ebenezer Ampaabeng from Ghana Broadcasting Corp.
Some nearby residents survived the fire, only to be swept away by the gushing waters.
"The loss of life is catastrophic, almost unprecedented," Mahama said.
Hours after the explosion, charred cars lay scattered across the gas station, some buried under collapsed roofs.
Mahama declared three days of mourning starting Monday. Flags will fly at half-staff during the mourning period.
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