Liverpool confirmed Becker has returned home due to a personal matter and is expected to rejoin the squad after they return to the UK.
According to The Athletic, the decision was made with the club’s full support.
The goalkeeper is one of several players who have departed the tour early, impacting new manager Arne Slot’s preparations for the upcoming season.
Becker said: “I have to thank the club for understanding the situation and giving me the time I need. I will be back with the team soon.”
He is the third player to exit Liverpool’s pre-season trip.
Forward Luis Díaz, 28, left earlier this week to finalise his £65.5 million transfer to Bundesliga champions Bayern Munich.
Defender Joe Gomez, 27, returned to Merseyside last week after suffering an Achilles issue.
He is currently undergoing medical assessment and remains a doubt for the early part of the campaign.
Liverpool, who arrived in Tokyo on Sunday following a 4–2 loss to AC Milan in Hong Kong, will now rely on summer signing Giorgi Mamardashvili to start in goal against Yokohama F. Marinos.
The 23-year-old joined from Valencia earlier this month and has impressed in training.
Freddie Woodman, Armin Pecsi and Kornel Misciur are also part of the squad in Japan and provide additional goalkeeping cover.
Slot’s side return to Anfield on 4 August for a home friendly against Athletic Club before facing Crystal Palace at Wembley in the Community Shield on 10 August.
Liverpool begin their Premier League title defence on 15 August at home to Bournemouth.
Slot, 45, is overseeing his first pre-season since succeeding Jürgen Klopp earlier this summer.
The Dutchman has already made several key signings, including Mamardashvili, with further additions expected before the transfer window closes.
The club’s pre-season campaign has been marred by high-profile departures and injury setbacks, but Slot is optimistic about building momentum ahead of the new campaign.