The ship was owned by a local shipbuilder near Sendai in Miyagi prefecture, local officials said.
A 10-metre tsunami hit Sendai, located near the quake's epicentre, at 3:55 pm (0655 GMT), washing away boats and cars and submerging residential areas and farms under muddy, debris-filled water.
City officials in Soma, Fukushima prefecture, also said a tsunami had surged about 5 kilometres inland there.
The Meteorological Agency said waves as high as 2 metres would hit wide areas of Japan's east coast.