The supporters blame Advocaat for the 3-2 defeat by the Czech Republic last time out, when he substituted lively winger Arjen Robben for defensive midfielder Paul Bosvelt with the team 2-1 ahead.
"The booing was because of the substitution the other day," said striker Kluivert, the Netherlands' leading scorer who has lost his place in the side to Ruud van Nistelrooy.
"For the Dutch people it was a mistake for the coach and that's why the jeering was so loud. I think you could say it was justified."
Kluivert, who has scored 40 goals for his country, said Advocaat could "hold his head up" after a week of fierce criticism of his tactics.
The Dutch qualified in second place from Group D to set up a last-eight clash with Sweden after the Czech Republic did them a huge favour by beating Germany 2-1.
However, Kluivert said he felt mixed emotions on a night of Dutch celebration.
"The trainer knows that I'm ready to play, I'm 200 percent fit and he knows that," said Kluivert. "The most important thing is that the team are through, I'm a team player, but I want to be playing.
"It's very frustrating and I've got contrasting sentiments even though this is a good night for us."
Kluivert was effectively relegated to third striker on Wednesday when Roy Makaay came on as substitute for man-of-the-match Van Nistelrooy, who struck twice to take his tournament tally to four.
Although Makaay scored, Kluivert is still hoping to play a part in his side's campaign in Portugal.
"This is where the tournament really starts," he said. "We have a lot of quality in the squad, so I will just have to wait and see if I can play a part.
"But I'm the leading scorer for my country and I want it to stay that way."
Kluivert, joint top scorer at Euro 2000 with five goals, has been told he can leave his club Barcelona.
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