Salaries of staff at public companies have come under attack from the frugal-minded Dutch public and politicians in recent years and the Rotterdam port's public shareholders decided to reduce the salaries of the five supervisory board members.
Scheepbouwer, chief executive of Dutch telecoms group KPN (KPN.AS) until April 6, resigned due to a "fundamental difference of opinion" with the shareholders regarding the establishment of a new remuneration policy for the port, the latter said in a statement.
A spokesman for the port added that Scheepbouwer had stepped down over the 5 percent pay cut.
In a dispute that has lasted almost two years, Dutch media earlier reported that Scheepbouwer argued that limiting salaries would result in the appointment of less-talented executives.
The Rotterdam port authority, which manages, operates and develops the Rotterdam port and industrial area, is 70.8 percent owned by the city of Rotterdam, while the Dutch state owns the other 29.2 percent.
Rotterdam is the largest European port for the import of crude oil, and the biggest port for iron ore supplies to the German blast furnaces in the Ruhr region.