Typhoon Nanmadol brought heavy rain as it cut across Japan and moved into the Pacific Ocean on Tuesday.
The storm killed two people and injured more than 100, halted traffic and left thousands of homes without power.
More damage was reported in southern Japan, where the storm made landfall at the weekend before weakening as it moved north, AP said.
On Tanegashima island, south of Kyushu island, a wall was damaged at Japan Aerospace and Exploration Agency’s space centre, the Economy and Industry Ministry said.
The extent of damage to the building used for rocket assembly was being assessed.
Two deaths were reported in Miyazaki prefecture on Japan’s southern main island of Kyushu on Monday, the Fire and Disaster Management Agency said.
A man was found in a submerged car at a flooded farm in Miyakonojo town, and another was found underneath a landslide in Mimata.
One person was missing in the western prefecture of Hiroshima, and 115 others were injured across western Japan, the agency said.
Most injuries were minor, with people falling down in the rainstorm, hit by shards of broken windows or flying objects.
More than 130,000 homes, most of them in the Kyushu region, were still without power on Tuesday morning, according to the Economy and Industry Ministry.
Many convenience stores were temporarily closed and some distribution of supplies has been delayed.
Most transport returned to normal on Tuesday, when commuters returned to work after a three-day weekend.
Bullet trains and most ground transport resumed, but dozens of flights were grounded in north-eastern Japan.
The tropical storm was on Tuesday in the Pacific Ocean off northern Japan, the Japan Meteorological Agency said.