Typhoon Lionrock was 170 kilometres (105 miles) east of the city of Choshi, as of 9 am (0000 GMT). Choshi lies straight east of Tokyo.
Packing wind gusts up to 180 kilometres per hour, the storm was moving north at 30 kilometres per hour and expected to make landfall in the northeast later in the day.
That would make it the first typhoon to directly land in the region from the Pacific Ocean since the country’s present weather observation system was introduced in 1951, according to the Japan Meteorological Agency.
Typhoons usually approach Japan from the south and southwest before moving northward across the archipelago.
Lionrock, which formed more than 10 days ago, has become the longest-lasting typhoon of those that have developed north of the 30th parallel north, breaking a 46-year-old record, according to the private Weathernews agency.
The previous record-holding typhoon in that category was in 1970, which survived for nine days and six hours, Weathernews said on its website.
Authorities have issued warnings for torrential rain, high waves, strong winds and flooding for the northeastern region, which remains vulnerable after destruction brought about by a March 2011 tsunami generated by a massive magnitude 9.0 offshore earthquake.
It is also expected to hit the region at high tide, deepening concerns for flooding along the coast from Tuesday afternoon through Wednesday morning.
Authorities also warned of landslides and high water due to expected heavy rain of up to eight centimetres per hour.
Some 110 domestic flights have been cancelled, public broadcaster NHK said.
Lionrock is expected to cut across the country’s main island of Honshu and head out to sea towards Russia and China, the Japan Meteorological Agency said.
The typhoon comes on the heels of two others that hit Japan in the past nine days, resulting in two deaths, the cancellation of hundreds of domestic flights and disruptions to train services.