Reports from Japanese media quoting local government officials say 9,500 people are unaccounted for in the northern coastal port of Minamisanriku.
Earlier reports said the death toll from the earthquake and tsunami was expected to exceed 1,300.
But this figure is expected to rise considerably as rescue teams probe the destruction.
A new earthquake measuring 6 has been reported at Fukushima, site of an earlier explosion at a nuclear power plant.
Japanese TV said it happened at 22.15 local time.
Earlier, the government played down fears over the explosion at the plant, saying that damage to the reactor was unlikely.
Dozens of aftershocks have followed Friday’s earthquake, including a violent 6.8 magnitude tremor recorded on Saturday, also off the country’s east coast.
New TV pictures show the impact of the tsunami – 10 metres high in places – that swept ferociously inland after the quake struck. Measuring 8.9, it was the strongest in Japan’s recorded history – the fifth largest to hit the world in the past century.
The images appear to confirm reports that trains were swept away, as carriages are seen lying among the debris.
Fires broke out in many areas including at an oil refinery.
There was some good news: more than 80 people on a missing boat were found safe and well.