TOKYO—It was the kind of provocation that has become familiar to Japan. On June 18, a Chinese submarine passed within a few miles of Japan’s territorial waters near the island of Amami-Oshima. Tokyo mobilized three destroyers and surveillance aircraft to make sure it didn’t stick around.

Breaking precedent, Japanese Defense Minister Taro Kono publicly identified the submarine as Chinese and said the incident was part of a pattern of China’s assertiveness that includes a recent border clash with Indian troops and a push to tighten its grip on Hong Kong.

China’s ascent has reshaped security policies across the Asia-Pacific region. Australia recently detailed $186 billion in high-tech defense spending over the next 10 years and, along with India, it is drawing closer to Japan and the U.S. through military drills and cooperation. South Korea is boosting spending on jet fighters after incidents such as one last year when Seoul accused Russian and Chinese bombers of intruding into its airspace and scrambled fighters in response. On Monday, the U.S. offered support to its allies in the region by formally opposing Chinese claims in the South China Sea.

Nowhere has the impact been stronger than in Japan. Its military is now one of the world’s best-equipped and trained, increasingly visible on exercises around the globe. A close partner of the U.S., Prime Minister Shinzo Abe has moved the country away from its strict pacifism during his 8½ years in power over two stints. China’s military rise, along with the threat of North Korean missiles, has been a major catalyst.

In March of last year, Japan opened military bases on Amami-Oshima, the island shadowed by the Chinese submarine, and on another island further south, both equipped with antiship and surface-to-air missiles. Another base is planned for a third island. In 2016, it added a military radar station on one of its islands closest to China.

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