This follows recent agitations by several business associations against the charges.
In a statement, the Transport Minister, Fiifi Kwetey is charging shipping lines to abide by the directive to enhance harmony in the shipping industry in Ghana.
According to the statement, the Ministry took the action after perusing a report on the matter from the Ghana Maritime Authority.
The Ministry said the charges cannot apply because there are a number of elements including stevedoring cost and pilotage which culminate in the freight price quoted by shipping lines.
Also, the Ministry argued that trade in Ghana has always had an all in freight which includes stevedoring and pilotage cost paid by shippers.
Again, the Ministry said no shipping service has not been introduced by the shipping companies at the ports in Ghana to warrant such new charges.
The statement, however, added that the shipping companies are at liberty to increase freight cost in line with their operational cost.
Meanwhile, the latest directive follows an earlier one that the shipping lines are said to have flouted and thereby reportedly causing several consignments of goods to be stuck at the ports as many clearing agents and importers were reluctant in paying the charges.
Some of the clearing agents spoke to JOY BUSINESS earlier about their concerns.
The latest directive for the shipping lines to withdraw should, therefore, be welcoming news for importers and the various business associations that resisted the implementation.