Ministry and agency officials were scrambling to respond to North Korea's announcement on Wednesday that the country had successfully tested a hydrogen bomb.
Senior Defence Ministry officials held two urgent meetings shortly after 11 a.m., with Defence Minister Gen Nakatani instructing them to quickly collect information about Pyongyang's claim.
Based on the instruction, the Air Self-Defence Force plans to collect airborne dust mainly over the Sea of Japan and Honshu to check for radioactive substances and other material related to nuclear experiments.
The ASDF was expected to fly a T-4 training jet equipped with a dust-collection pod to gather substances at altitudes of thousands of meters.
North Korea claimed its hydrogen bomb test was successful, but hydrogen bombs explode on a far larger scale than atomic bombs. The earthquakes observed were of a similar scale to earthquakes caused by North Korea's nuclear experiment in 2013.
"I wonder if the announcement that a hydrogen bomb experiment was conducted is true," a senior Defence Ministry official said.
Police on alert
After the first report of the possibility that North Korea conducted a nuclear test, the National Police Agency set up a headquarters to handle the issue at 10:53 a.m. Chaired by the chief of its Security Bureau in charge of North Korean affairs, the headquarters began collecting relevant information.
North Korea previously launched a long-range ballistic missile in the guise of a satellite launch and hinted it was conducting a nuclear experiment. The NPA has been exchanging information with relevant organisations from other countries.
"I thought the time would come sooner or later, but this is all very shocking," a senior police official said. "The incident will likely cause a certain degree of impact on the issue of abductions [of Japanese nationals by North Korea]."
To prevent disruption from spreading in the nation, the NPA instructed police in each prefecture to reinforce security on government facilities and those related to the pro-Pyongyang General Association of Korean Residents in Japan (Chongryon).
The Japan Coast Guard said that as of 12:30 p.m. Wednesday, there were no reports of damage to ships.
JCG Commandant Yuji Sato instructed all regional coast guard headquarters nationwide to take three actions: collect relevant information, vigilantly monitor and guard important facilities facing the sea and swiftly report any unusual activity.
"We're still confirming whether [the nuclear experiment] will affect ships and vessels currently at sea," a JCG official in charge said.
Officials from the Civil Aviation Bureau of the Land, Infrastructure, Transport and Tourism Ministry were busy checking facts related to the test.
"We'll confirm the extent the effects will have, and then respond appropriately," a senior transport ministry official said.
No clear S-waves
The seismic waves from the focus near North Korea were detected by the Japan Meteorological Agency, which is analysing the patterns assuming that the tremors were likely caused by a nuclear experiment - as was the case in the past.
"There are patterns similar to seismic waves in previous nuclear experiments," Yohei Hasegawa, director of the agency's Earthquake and Tsunami Observation Division, told reporters at 12:30 p.m. on Wednesday. "It's possible that the tremors are not from a natural earthquake."
In a natural earthquake, two kinds of seismic waves called S-waves and P-waves are released. P-waves occur first, followed by S-waves.
Hasegawa said S-waves were not clearly observed from Wednesday's event, and that the seismic wave patterns were similar to those caused by past nuclear tests.