Dutch police boarded the two ships of the environmental group, which had blocked the dock to prevent ships carrying coal from entering the port earlier on the day, Radio Netherlands reported. The two ships were brought to the quayside, where they were put under embargo.
The captains were arrested, but the protesters were released, the report said.
The Greenpeace action was part of an ongoing protest at the construction of a coal-fired power plant in Rotterdam's industrial area. The plant is one of the eight new coal-fired plants which German energy company E.ON plans to build in Europe.
Greenpeace says coal is the most polluting energy source.
On Saturday hundreds of environmental activists blockaded the construction site of the new E.ON plant. Dutch police intervened to end the protest.