The Welsh Rugby Union have announced that current Wales forwards specialist Robin McBryde will be interim head coach in Japan, with Edwards, Neil Jenkins and former Wales wing Mark Jones working as assistants.
Rob Howley, interim head coach for this season's RBS 6 Nations campaign and head coach Warren Gatland will be on British and Irish Lions duty in Australia.
Edwards had been strongly linked to a possible position with the Lions coaching staff, but Gatland will head up a team of Howley and England assistants Andy Farrell and Graham Rowntree.
Wales will play Tests against Japan in Osaka on June 8 and Tokyo seven days later.
And Edwards' presence on the trip has been described as "an added bonus" by WRU group chief executive Roger Lewis.
Lewis said: "The coaching team we have announced for the Japan tour is evidence of how the development pathway in Wales is working effectively for Welsh rugby.
"The group we have established represents an ideal mix of huge talent from the current Warren Gatland set-up, combined with some of our best young prospects for the future in a range of disciplines.
"To have young and emerging coaches and backroom staff learning from the likes of Shaun, Neil and Robin is a great opportunity for everyone selected to travel to Japan.
"Robin has already proved he can lead Wales successfully on tour and this time the presence of Shaun will be an added bonus which is bound to help our preparations."
McBryde led the Wales tour to North America in 2009, which took place when the Lions were touring South Africa and the Lions coaching team included Gatland and Howley.
"It is a privilege to coach my country, and I will embark on this tour determined to get the best out of the squad against what I know will prove to be tough opposition," McBryde said.
"It is inevitable that some of our leading players will be on Lions duty but the last tour I took charge of proved that it is possible to identify and blood some stars of the future in these games.
"I already have a great coaching relationship with Neil and Shaun but I am really looking forward to working closely with Mark Jones, who fully deserves this opportunity to step on to the international stage."
Jones is currently part of the Scarlets coaching set-up headed by former Ireland flanker Simon Easterby.
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