He said neither the skipper nor any other victims have been found, more than two hours after the collision occurred at 7 a.m. local time.
The ferry is used to shuttle pedestrians and often their bicycles across the Amsterdam-Rijnkanaal, a broad, heavily used internal waterway.
Divers are in the water looking for victims and a helicopter is using infrared sensors to search the water for warm spots. The incident took place near the town of Nieuwer Ter Aa, roughly 6 miles (10 kilometers) south of Amsterdam.
Photos of the boat published by NOS Friday showed it floating upside-down near the side of the canal, a brown-red bottom facing upward and a life preserver drifting in the water nearby.
Video footage of the boat taken last summer and posted on YouTube show it is big enough to fit around a dozen passengers, and not big enough to carry a car.
Traffic on the canal has been halted. The boat's owner, SwetsODV, said on its Twitter feed Friday that the boat, identified as AA, is "out of commission." The company could not be reached for comment.
Zuiderhoek said maritime police have opened an investigation into the cause of the accident, which is not yet known.