At the start of this month, Russia beat England, Spain-Portugal and Netherlands-Belgium to win a ballot of FIFA's 22-strong executive members in Zurich for the rights to host the 2018 World Cup.
Qatar then saw off bids from South Korea, Japan, Australia and the United States for the 2022 tournament, but Beckenbauer says he was disturbed after details of the voting were later leaked.
"I have less confidence in FIFA," the German legend told daily Bild. "I'm disappointed how FIFA handled things after the voting.
"The seven losers were all left in disgrace. Especially England and Australia."
England won only two votes out of a possible 22, while Australia picked up just a single vote, prompting a huge media backlash by the British media over the failure of the English bid.
Beckenbauer is set to stand down from the executive committee next March, but he says FIFA's conduct in the wake of the decisions has left a bad taste in his mouth.
"The executive members were told that neither us nor the public know the exact number of votes," he said.
"We were only told after each round of voting, which countries were left. And then I hear a couple of hours later on the radio, which countries received which share of the votes."