Samuel, who ploughed more than Â£3m into the old Bridgend club and claims to have pumped more than Â£1m into the Warriors this season, says he is quitting because of a lack of support from the fans in the new Bridgend/Pontypridd region.
Samuel is one of two directors from the Bridgend club who sit on the Warriors board of directors. The WRU provides the other two.
"The WRU have two people on the Warriors board - Steve Lewis and David Rees - and Mr Samuel has not discussed this issue with them," said Moffett.
"I'm extremely disappointed that such a serious and significant statement was made to the media before it was discussed at board level.
"I'm not prepared to comment further until the issue has been debated by the Warriors board."
Mr Moffett also said "depending on what was agreed", he may have to call a special meeting of the WRU board to discuss the matter.