The new Self Defence Force base on Yonaguni is at the western extreme of a string of Japanese islands in the East
China Sea, 150km south of the disputed islands known as the Senkaku islands in Japan and the Diaoyu in China.
"This radar station is going to irritate China," said Nozomu Yoshitomi, a professor at Nihon University and a former major general in the Self Defence Force.
In addition to being a listening post, the facility could be used as a base for military operations in the region, he added.
The deployment fits into a wider military build up along the island chain, which stretches 1,400 km from the Japanese mainland.
Policy makers last year told Reuters it was part of a strategy to keep China at bay in the Western Pacific as Beijing gains control of the neighbouring South China Sea.
Toshi Yoshihara, a US Naval War College professor, said Yonaguni sits next to two potential flash points in Asia
Taiwan and the Senkaku/Diaoyu Islands.
"A network of overlapping radar sites along the island chain would boost Japan's ability to monitor the East China Sea," he added.
Yonaguni is only around 100km east of Taiwan, near the edge of a controversial air defence identification zone set up by China in 2013.
Over the next five years, Japan will increase its Self-Defense Forces in the East China Sea by about a fifth to
almost 10,000 personnel, including missile batteries that will help Japan draw a defensive curtain along the island chain.
Chinese ships sailing from their eastern seaboard must pass through this barrier to reach the Western Pacific, access to which Beijing needs both as a supply line to the rest of the world's oceans and for naval power projection.
To mark the start of operations, Japan's military will hold an opening ceremony on Monday. The 30 sq km outcrop is home to 1,500 people, who mostly raise cattle and grow sugar cane. The SDF contingent and their families will increase the population by a fifth.
