Three people were reported killed, hundreds of plane flights cancelled, and train services disrupted in the wake of Typhoon Lan.
Recent opinion polls show Abe’s support plunging to below 30%, its lowest since he returned to office in 2012 with a promise to revive Japan’s economy.
Some 7,500 rescuers, including police, firefighters and soldiers from Japan’s Self Defence Forces, were mobilised to help with evacuations and search for the missing.
The abdication, the first since 1817, appears to have support among the general population, who view it as a sign of changing times.
Masahiro Imamura was forced to quit after he said that it was better the massive 9.0 earthquake that killed nearly 20,000 people happened in the northeast.
The controversy is the biggest crisis to face Abe since he returned to office in 2012 for a rare second term, eroding his support rating.
“As a symbol of the state and the people of Japan, I will share their pain and their joys, praying for their happiness,” Naruhito told reporters in Tokyo.
When a magnitude 7.4 quake hit the same area, the country swung into action, using lessons learned in the March 11, 2011 disaster.
North Korea’s Atomic Energy Institute, which has jurisdiction over the country’s Yongbyon nuclear facilities, also told Kyodo it had been producing highly enriched uranium necessary for nuclear arms and power “as scheduled.”
Critics say the Liberal Party’s attention towards LGBT rights has more to do with improving its international image than social justice.
Although the intensity of the earthquake on the Japanese scale matched that of the March 2011 quake that left nearly 20,000 dead, the absence of a tsunami and Japan’s strict building codes helped keep the death toll down.