The Dutch Finance Ministry said on Thursday it was "disappointed" with an EU Commission order to do away with corporate tax exemptions for six ports, including Rotterdam, Europe's largest.
The measure puts the Netherlands at a disadvantage, the government said in a statement, calling on the Commission to ensure fair competition.
European Union regulators told Dutch authorities on Thursday to scrap a corporate tax exemption for the ports and also ordered Belgium and France to align their port taxation systems with the bloc's state aid rules.
"The Commission's decisions today regarding the Netherlands, Belgium and France make clear that if port operators generate profits from economic activities these should be taxed," European Competition Commissioner Margrethe Vestager said.
The port companies to be taxed from January 2017, are Groningen Seaports N.V., Havenbedrijf Amsterdam N.V., Havenbedrijf Rotterdam N.V., Havenschap Moerdijk, N.V. Port of Den Helder and Zeeland Seaports.
The Dutch case came about after the government passed a law in June that subjected public entities to corporate tax starting from January 2016 with the exception of the ports.
A generous Dutch corporate tax climate helps dozens of the world's largest business lower tax rates to a single digit. It has also been criticised by the Organisation for Economic Cooperation in Europe (OECD).
The Netherlands has appealed another Commission ruling, ordering it to claw back millions in tax from coffee giant Starbucks.
Reporting by Anthony Deutsch