Off the field he has been instrumental in developing the operational structure of the WRU's medical welfare systems during almost two decades of dramatic change as the game moved into the professional era.
The WRU is to appoint a new National Team doctor while Professor Williams takes on responsiblity for matchday medical facilities at the Millennium Stadium and liaison with key IRB committees on behalf of the WRU.
Since 1996 his work with the WRU has developed in parallel with his full time medical career which has treatment and internationally renowned research initiatives.
He is the retiring Professor of Medicine and Professor of Nephrology at the University Hospital of Wales College of Medicine in Cardiff.
Through his passion for rugby he joined the WRU in an honorary role as the A Team doctor from 1996 until 1999 when he also took on National Team duties.
During his tenure with the senior Wales team, Professor Williams worked with colleagues to construct and install medical care systems and initiatives appropriate for the developments with the elite game.
WRU Group Chief Executive, Roger Lewis, said: "Professor John Williams can be proud of the excellent service he has given to Welsh rugby through such an important chapter of its history.
"He has been instrumental in setting in place systems and structures which met the demands of the enormous changes happening within the modern game and we are all delighted he will be continuing to play a key role in the WRU medical structure."