Local media report that the attackers opened fire during the Tuesday morning incident.
They also held a security guard hostage at gunpoint before beating up some drivers at the station.
Security forces have been deployed to restore calm.
On Friday, a group calling itself the Western Togoland Restoration Front attacked two police stations and exchanged fire with security officers, killing one person and leaving five others injured.
The separatists also stole 10 AK-47 assault rifles and a police vehicle in what is considered the most daring attack by the group. A manhunt has been launched for its leaders.
Five different groups have been campaigning for decades to form a new country called Western Togoland – made up of parts of Volta region and northern Ghana.
They claim the region has been marginalised by successive post-colonial administrations.
British-administered Togoland did not fall within the borders of the formerly Gold Coast region – which now defines most of modern-day Ghana.
Now the territory wants its independence restored.
The latest string of attacks could pose a serious security risk as Ghana holds its elections in December.