At around 11:45pm on October 11th,[fn 1] after 95mm of rainfall from Typhoon 21 within the previous 24 hours, a 120-meter length of the station structure had bulged upward by up to 1.3 meters.

[fn 2] Gaps of up to 70cm opened in the retaining wall seams, and sediment-laden groundwater began pouring in at up to 8 tons per minute.

To lower the groundwater level, eight deep wells were drilled, and 8 tons of water per minute were discharged into the sewer system.

By the middle of November, the groundwater had subsided enough for construction to reach full speed, and by December 11th, the station was restored.

[4] At first, restoration had been expected to take 6 months, but in view of the Musashino Line's importance for freight transportation, construction was expedited and carried out around the clock.

This effect caused frequent inundation in the town of Nishi-Koigakubo, in Kokubunji, but it was reduced by the measures JR East took to protect Shin-Kodaira from flooding.

[8] During the two months it took to restore service, the Musashino Line operated in two segments:[4][9] between Tokyo or Shin-Narashino and Shin-Akitsu, and between Nishi-Kokubunji and Fuchūhommachi.

[4][9] This created chronic congestion in the towns of Kumegawa and Koigakubo, along Tokyo Metropolitan and Saitama Prefectural Route 17, and meant that it could take around an hour to travel between two stations.

There was a plan to introduce a temporary connecting passageway between Shin-Akitsu and Akitsu stations,[10] but it was dropped amid opposition from local merchants, who feared it might become permanent.