The only player to win the World Cup three times was dismayed by recent games in which home fans barracked Brazil's players and their manager Luiz Felipe Scolari.
"This is a team that is under construction, this is a 15-day tournament, so let's not boo them," Pele said to applause at a promotional event in Sao Paulo.
"Let's support the players, even if things don't work out because this is us preparing for the World Cup."
The eight-team Confederations Cup takes place in Brazil from June 15 to June 30 and is considered a major test run for next year's World Cup, both for players and organisers.
More than 80 percent of the tickets have been sold for this month's tournament and it promises to be the most successful ever commercially.
Brazilian fans have a reputation for colour and flamboyance when overseas, but at home they are demanding and fickle. As the only team to win the World Cup five times, Brazilian supporters are unforgiving when their expectations are not met.
In last week's 2-2 draw against England it took fans just 12 minutes before they were hounding their own players. They also greeted Scolari's second-half substitutions with chants of "Donkey, Donkey".
Fans were more positive in Porto Alegre on Sunday when Brazil overcame a France 3-0 in a friendly.
But Pele warned the team were not the finished article and said they must improve if they are to win next year's World Cup on home soil.
"We are prepared for the Confederations Cup, but the World Cup is another story," agreed Carlos Alberto Torres, the captain of Brazil's 1970 World Cup-winning side. "We have another year to prepare for that."
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