The WRU confirmed it was in relation to a potential breach of betting on rugby.
World Rugby's regulation 6.3.1 reads: "No connected person shall, directly or indirectly, bet and/or attempt to bet on the outcome or any aspect of any connected event and/or receive and/or attempt to receive part or all of the proceeds of any such bet and/or any other benefit in relation to a bet."
Wales have sent for Stephen Jones to fill the gap left by Howley's sudden departure and Jones is expected to arrive "imminently" at the squad's Kitakyushu base.
The WRU statement said: "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 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. Rob has co-operated fully with our initial discussions. Warren Gatland has consulted with senior players and Stephen Jones will be arriving in Japan imminently to link up with the squad as attack coach."
Source: GMB / BBC