Only six hours later, the storm intensified into a typhoon and underwent rapid intensification into a modern-day Category 4 super typhoon just east of northern Luzon in the Philippines with maximum sustained winds of 130 knots (240 km/h; 150 mph) calculated in 1-minute sustained winds along with JMA's estimates of its minimum pressure of 910 millibars (27 inHg) on September 7.

However, it started to weaken below super typhoon status, and its intensity began to fluctuate while moving northwestwards and north-northwestwards.

As it turned northwards by September 12, June regained its intensity as a Category 4 system before making landfall over Yamaguchi Prefecture's Shimonoseki City.

As the typhoon further approached and made landfall over Japan, public infrastructures including bridges and highways sustained damages.

Along with Typhoon Lorna that struck Tokyo-Yokohama area, June were responsible for over $300 million (1954 USD) worth of damages.

Despite the findings of the FWC, the JMA found the typhoon even stronger than earlier, with 910 millibars (27 inHg) being reported at this time.

[2][3] Reconnaissance aircraft examined the system by September 10, and found that June has nearly the same size as Grace in that season, with over 300-mile radius.

[2][3][6] It then moved just west of Yakushima Island before making landfall over Shimonoseki City in Yamaguchi Prefecture by the night of September 13.

The agency would stop monitor the storm at 12:00 UTC of September 15; however, the JMA continued to track the typhoon's remnants until the same time of the next day.

Over Camp Bofu at Kokura, 49 children and women were asked to move out of the area, from the order of a high-ranked military officer.

[6] First reports from the storm in Kyushu and Shikoku from the Japanese National Police registered one death and missing each and three injuries somewhere the aforementioned regions.

The storm's rainfall also disrupted the ongoing strike by the country's national employees over the military bases in Japan's south.

The construction ministry of the country also placed the first estimates of the damages in government establishments and equipments from the typhoon to be at $4 million (1954 USD).

Cloudy weather with some downpour were also experienced in some areas of Siberia due to the remnants of June, including Vladivostok.

[14][15][16] The Korean Peninsula also didn't escape June's impacts, where areas over the region received torrential rainfall from the storm.

This incident forced the troops of Republic of Korea and United States’ air base to move into a higher place.

[17] Around Seoul, soldiers there and civilians were also alerted of the Han River increasing its water level for the second time after it did so in the morning of September 15.

[20] On September 16, stranded soldiers at the Camp Taro Leaf somewhere the peninsula were brought food via air, as highways were still not passable.