"I want to thank Josh for the dedication, energy and vision he has brought to his role as Head of Rugby," WRU Group Chief Executive Martyn Phillips said.
"There is no doubt his principle achievement across the past two years has been to drive strategic change and put in place a club hub structure which is already proving successful in introducing a new core of young players into the game."
The 38-year-old, England's 2003 World Cup-winning full back, said he had decided for personal reasons to quit the role he took in 2013.
"I came to work here with a specific focus in mind, seeing the opportunity and need to address the underlying structures whilst the national team were so successful - to attempt to 'fix the roof while the sun is shining'," he said.
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"My family are from Wales and I know the difference sport, but especially rugby, can make to people’s lives and local communities.
"To avoid speculation there have been some developments over the last year relating to personal matters, meaning I couldn’t continue to be in Wales on a full time basis."
(Writing by Ken Ferris; editing by Alan Baldwin)
