As of 3 p.m. Wednesday, the typhoon was traveling northwest in the sea south of Okinawa at a speed of 15 kilometers per hour, with an atmospheric pressure of 940 hectopascals at its center and packing winds of up to 234 kph, according to the agency.
The entire nation will be affected by Typhoon Kong-rey into Saturday, Sunday is forecast to be dry and bright but expect cooler temperatures to set in.
Waves have been reported surging over 22 feet as the swirling storm system tracks across the ocean.
Super Typhoon Kong-rey is now located around 1,000 kilometres south-southeast of Okinawa.
When it lands, Kong-rey is expected to have wind speeds of approximately 75 miles per hour - the equivalent of a Category 1 hurricane, CNN reported.
Earlier this week, Typhoon Trami battered Japan, killing two and injuring more than 120 people.
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Soon she was petting and stroking the elephants, smiling and laughing and having a good time. "It is a attractive thing to see". Quickly, people across the globe slammed her because the hat was similar to the one used by colonial masters in Kenya.
Japan's 25th typhoon of the season is forecast thereafter to move over northern Japan over the three-day weekend, with the weather agency saying the requisite alerts will follow as necessary.
It was the strongest typhoon since Typhoon Yancy hit in 1993.
Dress warm tomorrow as there will be strong gusty winds, . most places beginning the morning in the mid to high teens.
Richard Miles, spokesman for the UK's Met Office said: "It could damage infrastructure and bring a risk to life, mainly as a outcome of flooding and landslides".
Southern Kyushu and the Amami island chain may see rainfall of up to 150 mm, the JMA said.