The numbers of confirmed deaths and people reported missing have been rising. According to the National Police Agency, as of 20:00 local time, there were 3,373 dead, and 6,746 missing. However, authorities and the press are agreed that these figures will increase quite drastically.
For those in the shelters, there is a bad news: the weather is set to become much colder from tonight. The SDF (Self Defence Force) are trying to deliver as much food, water, blankets, etc as possible to the shelters. It is estimated that around 520,000 people have sought shelter at over 2,500 locations. The logistics for aid have been unified, and placed under the direction of the SDF, who will be responsible for transport.
A note on the sources
I have relied on information available at Japanese internet sites, mainly asahi.com and Yomiuri Online, the two largest daily newspapers in the country, and Kahoku Online Network, a regional paper, as well as official sources, such as Japan Meteorological Agency and the National Police Agency.