The toll was expected to increase substantially once all bodies wash ashore in the disaster-hit northeast and those buried in rubble are recovered and identified. That will start when seawater recedes and the tsunami warnings are lifted.
The police agency said the confirmed death toll was from the 12 prefectures hit by the twin disasters, Kyodo News reported.
The agency also said 7,843 people remained unaccounted for as of Wednesday in six prefectures.
Currently, about 80,000 police officers and personnel from Japan's Self-Defense Forces are involved in rescue and relief operations in the region.
But those efforts were being hampered by cold temperatures.
The Kyodo report said autopsies on the victims are going slowly because of a personnel shortage.
The report said police in the worst-hit Miyagi prefecture were considering volunteers to work with victims' families so police can be freed to perform autopsy work. Some identification of victims was being made from recovered belongings.
The government said about 530,000 people were now accommodated in shelters.