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He had a possible breach of World Rugby's rules about betting, the Welsh Rugby Union said.
The 48-year-old missed Wales' welcoming ceremony in Kitakyushu on Monday and will be replaced in Japan by former first five-eighth Stephen Jones, the WRU added.
"The WRU can confirm that Rob Howley has returned to Wales to assist with an investigation in relation to a potential breach of World Rugby regulation 6, specifically betting on rugby union," the governing body said in a statement.
"The decision was taken to act immediately in light of recent information passed to the WRU.
"No further details can be provided at this stage as this would prejudice the investigation. If required an independent panel will be appointed to hear the case."
Wales start their World Cup Pool D campaign against Georgia on Monday.