He will leave his post on 31 December to live in New Zealand.
Moffett joined the WRU in December 2002 and set about reducing close to £60million of debt and overseeing Wales' move towards regional rugby.
Under his stewardship the WRU has turned a £3.7million annual loss into a pre-tax profit of £3.6million for 2004/2005.
Moffett said: "My reasons for leaving are personal and family and I don't have another job to go to, but we will be returning to live in New Zealand.
"In many respects it's a lot like Wales and we've loved every minute of living in Wales, but our families are down in that part of the world."
In March 2004 Moffett signed a four-year extension to his initial contract - thought to be worth more than £200,000 a year - which was set to take him up until 2008.
The WRU will not replace Moffett, instead asking WRU general manager Steve Lewis and Millennium Stadium general manager Paul Sergeant to take over the responsibilities jointly.
