Kerry travel to Newcastlewest (7pm) for their Munster championship opener against Limerick but will be without the two players who captained the county to 2016 and 2017 All-Ireland minor success.
Under general rule, any player who is selected on a 26-man senior championship squad is ineligible to play in an U20 match in the same year.
Limerick’s Josh Ryan is also precluded from featuring in this evening’s quarter-final having been part of the Limerick senior squad for both of their championship defeats to Clare and Limerick.
Whelan said it would have been “the lesser of two evils” were Clifford and O’Shea allowed train away with the seniors and then fall back in with the U20s on matchday.
“Going back through the years, some of the great Kerry players would have had great success at minor and U21 before going onto senior. Ironically, David and Seán captained the last two All-Ireland winning teams.
"They’d be a loss to the senior team if the seniors didn’t have them. So you can imagine how much of a loss they are to us.
“I’d be disappointed with the ruling. If a player is U20, they should be able to play with their own comrades at their own grade. From a county perspective, however, the right decision has been made.
"If these lads are good enough to play senior, there is only one gig in town — that is the Sam Maguire Cup.”
Eight of the Kerry squad have been focused on their Leaving Cert this past week and a half, with Diarmuid O’Connor sitting his final exam this afternoon.
Whelan believes the start of the Munster championship could have been put back a week to allow players finish exams.
“It has been difficult enough to get the players together. Even when you are trying to have a last A v B game, there are eight guys doing their Leaving Cert and that’s the most important thing at the moment.
"With regard to third-level exams, they all fell at different times so lads in UCC and UL were doing them a week earlier to players in Dublin. We’ve managed it as best we could.
“For the first year of U20, their attempt to put it on the calendar at the best possible time was not a bad one. One week would have made a difference.
"We have one guy doing an exam [today]. It is very hard to see how he could be mentally prepared to go out and play a few hours later.”
M O’Callaghan (Ballylanders); C Ferris (Ballysteen), K Maloney (Crecora Mainister), A Riordan (Fr Caseys); O Collins (Adare), D Enright (Monaleen), L Woulfe (Newcastlewest); R Childs (Galtee Gaels), C McSweeney (Gerald Griffins); P McGrath (Galtee Gaels), A Storan (Mungret St Pauls), L Kennedy (St Kieran’s); C Moran (St Patrick’s), A Kearns (St Senan’s), B Coleman (Rathkeale).
D Uosis, (Dingle); D Naughton, (Dr. Crokes) S Okunbar, (Na Gaeil), M Reidy, (Ballymacelligott) M Breen, (Beaufort) G O’Sullivan,(Piarsaigh na Dromoda) D O’Brien, (Glenflesk) M Ryan, (Rathmore) D O’Connor, (Na Gaeil) F Clifford, (Laune Rangers) C Linnane, (Beale) D Moynihan, (Spa, Killarney) D O’Sullivan, (Kilgarvan) B Sweeney, (Listowel Emmets) D Shaw, (Dr. Crokes). Subs: B Lonergan, (Ballymacelligott), P Warren, (Gneeveguilla), B Friel, (Rathmore), M Foley, (Ballydonoghue), E Horan, (Scartaglen), S O’Leary, (Kilcummin), C Gammell, (Killarney Legion), M Potts, (Dr. Crokes), C Kennedy, (Beaufort).