However, France and Belgium do not have to recoup unpaid tax as the exemptions were in place before the two countries joined the European Community, reported IHS Media.
Belgian ports, including Antwerp, pay less tax than other companies and French ports, including Le Havre and Marseille, are fully exempt from taxes, in breach of EU state aid rules, the commission said.
"The commission decisions for Belgium and France - as previously for the Netherlands - make clear that unjustified corporate tax exemption for ports distort the level playing field and fair competition. They must be removed," EU competition commissioner Margrethe Vestager was quoted as saying.
The commission eased state aid rules for member governments' investments in ports in May to cover the costs of dredging and access to waterways.
Governments can invest up to EUR150 million (US$175.5 million) in sea ports and EUR40 million in inland ports without having to seek approval from Brussels' regulators.