Warburton's Cardiff Blues contract is due to expire later this year.
The central contract with the WRU, seen as a way to stop Welsh talent moving overseas, will mean Warburton can be loaned back to the Blues at no cost to the club when he is not needed for international duty, provided the WRU secures an agreement with the four domestic regions.
The political divisions in Welsh rugby have led to Warburton, who has not played since November due to injury, suffering online abuse accusing him of being a "scab" and betraying his club.
"Some of the uninformed vitriol aimed at my client has been disgraceful," Warburton's agent Derwyn Jones told The Times newspaper.
The abuse came despite the fact Warburton could have followed the likes of Leigh Halfpenny out of the domestic game.
The fullback left the Blues this month for French Top 14 side Toulon who, along with Stade Francais, was a potential destination for Warburton.
A move to either of those clubs could have earned the Wales captain around 700,000 pounds a season, The Times reported.
POLITICAL FALLOUT
"I cannot comment on many aspects of Sam's contract negotiation process due to client confidentiality but the broad facts are as follows: Cardiff Blues and the WRU could not table a joint offer for Sam because of the current political fallout between the Welsh regions and the WRU," Jones said.
"Cardiff Blues alone could not give Sam a market value contract offer due to the uncertain future of the game in Wales. They also could not offer this to Leigh Halfpenny who has since signed for Toulon.
"Sam was faced with the following two options regarding his playing future: pursue interest from two teams in the French Top 14 at twice his UK market value (or) sign a three-year employment contract with the WRU to stay in Wales at his UK market value."
Warburton decided to remain in Wales because of his affection for Cardiff and the fact he is captain of the national side who will launch their bid for a third consecutive Six Nations title when they meet Italy on Saturday.
"At this time, however, due to the current fallout between the regions and the WRU, there are no cast iron guarantees that Sam will be able to play for Cardiff Blues next season," said Jones.
"Sam wants to stay in Wales and intends to play for Cardiff Blues next season should all the issues be resolved. But if he had moved to France there would have been absolutely no chance of him playing for the team he has supported since he was a young boy.
"He also prefers staying in Wales over moving to France as he is passionate about maintaining the Wales captaincy. Sam appreciates that playing for Wales is a privileged position and does not, in any way, take this for granted."
($1 = 0.6060 British pounds)
(Reporting by Josh Reich; editing by Tony Jimenez)
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