The Catalans are set to meet Athletic Bilbao in the showpiece event and that has raised alarm bells in the Spanish capital given that the last time the two sides met in the tournament decider, in 2009 at Mestalla, certain fans from both clubs booed the national anthem.
Guardiola thinks that the Bernabeu is the ideal venue for the final but is aware that staging the game there could cause controversy.
"It is a fantastic stadium and has a large capacity, but I understand the reluctance of Madrid to host the game against Athletic there," the former Spain international told reporters during his press conference ahead of Saturday's clash with Osasuna.
"I understand that in a final, if there is no predetermined venue like in the Champions League, you must seek out a neutral setting.
"So, I would not like to play the final at San Mames [home of Athletic Bilbao] because it would be an advantage to our rivals. But it will be the [Spanish Football] Federation who decides."
Meanwhile, after it was pointed out to him during his press conference that Barca had lost just one of their 40 games in all competitions so far this season, Guardiola pondered the fickle nature of the footballing press.
"A fortnight ago this was the worst year of Pep and now it is the best," he exclaimed.
"I would have rather lost more games and drawn less in order to be closer to the [La Liga] leaders [Madrid], but the balance is good.
"We have won three titles, we have played some good games and where we did not win, we competed well.
"Some teams will play as many games in a year as we're playing in February. But it is still not enough to have lost only one game if someone else is ahead. "
Barcelona currently sit second in La Liga, seven points behind Madrid ahead of Saturday's trip to Pamplona.
Starting in November and continuing through to the middle of February, Goal.com is publishing exclusive extracts from Graham Hunter's highly-anticipated new book, 'Barca: The Making of the Greatest Team in the World'. The last extract looked at how Barca suffered rare disappointment at the hands of Real Madrid in a gripping finale to last season's Copa del Rey. Don't miss it!