The storm has been strengthening over the Philippine sea and reached Super Typhoon status, meaning it has sustained winds of over 150mph.
It could get more intense still, but is expected to weaken before it hits the islands late on Thursday or Friday local time.
Meteorologist Danielle Banks from The Weather Channel said: “There could be substantial rain, damaging winds, high seas and the flooding and mudslide threat.
“And remember, this one is coming on the heels of Typhoon Trami.”
Super Typhoon Kong-Rey is expected to be steered northwestwards over the next few days and vertical wind shear to deplete its strength.
It will then likely make a sharp turn towards the northeastern direction.
By the time Kong-rey makes landfall it may be looking at wins of 80mph, a category 1 typhoon.
Parts of Taiwan, China and Korea could also be at risk from the storm and have been warned to keep track of it.
AccuWeather Meteorologist Rob Richard said: “After threatening the Ryukyu Islands, scenarios for Kong-rey’s expected track around the start of the next weekend range from the Typhoon targeting Taiwan and/or eastern China or curving northwestward to mainland Japan or the Korean Peninsula.”
Over the weekend, the Kong-rey brought rain, gusts and high surf to Guam, a US territory in the western Pacific.
This new threat comes just days after Typhoon Trami devastated Okinawa, causing widespread damage and power cuts, killed two people and injured around 120.
It brought 125mph winds to southern parts of the island on Saturday, according to the Japanese Meteorologist Agency.
Nearly 3.7million people were advised to evacuate ahead of Trami and around 1,000 flights were cancelled.
Kong-rey, which could also affect Okinawa, marks the next storm in this year’s relentless typhoon season.
Last month, Super Typhoon Mangkhut hit the northern Philippines with category 5 intensity, causing floods and deadly landslides and also affected southeastern China and Hong Kong.
Before that, Typhoon Jebi caused extensive wind damage and storm surge in Japan.