The Welsh Rugby Union (WRU) confirmed Howley has returned to Wales six days before the team's opening World Cup match against Georgia in order to "assist with an investigation in relation to a potential breach of World Rugby regulation 6, specifically betting on rugby union".
A WRU statement said: "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 and we would ask that the media appreciate this is a difficult and personal matter for Rob and that his privacy is respected before an outcome is reached.
"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."
Howley has been a key member of Gatland's backroom staff and oversaw their 2013 Six Nations success while the New Zealander was on a British and Irish Lions sabbatical.
The former Wasps scrum-half was part of Gatland's coaching team when the Lions triumphed in Australia in 2013 and drew a series against the All Blacks four years later.
The 48 year-old will leave his role with Wales when Gatland departs after the World Cup and had been touted as a potential replacement for Conor O'Shea as Italy boss.