Munster officials visited and inspected Waterford's home venue recently and it is currently undergoing redevelopment but it was still not felt adequate to host the glamour tie.
The first semi-final, between Tipperary and Limerick, will also take place in Thurles a week later (June 1) and All-Ireland champions Clare will meet Cork or Waterford in either Thurles or Limerick on June 15, with the Munster final set for July 13.
In Munster senior football Tipperary will have to travel to Limerick for their quarter-final on May 31 and Clare will have home venue for their quarter-final with Waterford on June 6 or 8.
If Cork play Tipperary in their semi-final they will have home advantage but if it is Limerick the Rebels will have to travel to the Gaelic Grounds.
And Kerry will have to travel to Clare or Waterford for the semi-finals, which will take place on June 21/22 with the Munster final fixed for July 7.
Meanwhile, Armagh and Down will meet under the Athletic Grounds lights on Friday, February 7.
Elsewhere, former Erne star Raymond Johnston has joined Peter McGrath's new back-room team in Fermanagh as a selector.
Waterford dual star Wayne Hutchinson will play exclusively for their footballers next season.