The RFEF said the clash between Barcelona and Sevilla, which this season is being played as a one-legged tie in Morocco, is not classed as a competitive game.
That means Barcelona will not be restricted in the number of non-European Union players it can name in its squad on Monday (AEST), potentially making new signing Arturo Vidal more likely to feature.
Philippe Coutinho has also reportedly been granted a Portuguese passport, meaning the Brazil international no longer counts as one of Barca's non-EU players.
Valverde questioned why the RFEF made the decision on the eve of the game and he suggested Spanish football's governing body has made the wrong call.
"As for the Supercopa not being a professional competition, I do not know what to tell you," he said.
"I think that Sevilla are professionals and we are professionals. With all the trouble we have had this week with non-EU squad members, they could have warned us before.
"That it is a single match adds difficulty. Last year we lost the Supercopa [5-1 on aggregate to Real Madrid] and started LaLiga well."
Vidal's arrival from Bayern Munich has bolstered the Barca midfield after the departures of Paulinho and Andres Iniesta.
But Valverde, whose squad has had defender Clement Lenglet and uncapped Brazilians Arthur and Malcom added since the end of the 2017/2018 season, denied reports suggesting he demanded signings of Barcelona's board.
"We're good with what we've got. It's evident we'll be alert to what could happen in the transfer market but we're happy how we are and we haven't asked for anyone else," Valverde said.
"In that moment I said we'd need another midfielder of similar characteristics to Paulinho. Arturo Vidal is here now and that's it. I don't believe I've said anything else about the topic.
"Last year one of our important players left [Neymar joining Paris Saint-Germain for a world-record €222million] and we had to react. You all know how this works and we must be prepared for everything.
"I'm not closing the door on anybody, but I'm only focused on the players I have and I must say I'm very satisfied with the squad here."
Of Ousmane Dembele's future, the France forward having been linked with a loan move, Valverde added: "I do not know if there is an option or there is no option.
"I count on him and I'm not thinking of any player leaving. We have the ones we have here, I'm not thinking of players leaving."