The explosion in the Legon suburb of north-west Accra on Saturday was followed by a secondary blast, and there were a number of casualties, authorities said.
Ghana's deputy information minister Kojo Oppong-Nkrumah said the fire had been controlled and firefighters were now controlling the second explosion.
"It is early days yet to give any figures" on the number injured or dead, he said, adding there were casualties.
More than 200 police personnel were also deployed to help cordon off the area of the explosion, making it difficult to access.
The filling station is near a transport terminal and close to some hostels for the University of Ghana in Accra.
George Agbey, who was close to the scene of the explosion, said: "There was some panic and we all just moved away from the scene. It was like refugees moving away from a war-torn zone."
In May, an explosion at a factory in the Western Regional capital of Takoradi happened as a tanker was discharging liquefied petroleum gas at the Ghana Household Utilities Manufacturing Company factory.
That explosion killed at least six fire service personnel at the scene, and injured at least other 80 people, according to Ghana's state news agency.