The football governing body president claims the allegations surrounding the 2022 World Cup bid are motivated by discrimination.
Qatar was chosen to host the tournament in December 2010 but Fifa have begun an internal inquiry after corruption claims repeatedly surfaced, with the latest claims from the British media suggesting millions were exchanged to secure votes.
"There is a sort of storm against FIFA relating to the Qatar World Cup," Blatter told reporters Monday. "Sadly there's a great deal of discrimination and racism."
"It really makes me sad," he added.
FIFA will decide on the validity of the bidding process for the 2018 and 2022 World Cups in September or October and Blatter said, at this point, the "matter will be closed".
Meanwhile, at its general assembly in Sao Paulo, the Confederation of African Football (CAF) criticized what it labeled "the repeated, deliberately hateful, defamatory and degrading attacks by some media, notably British, on the image and the integrity of the Confederation of African Football, its president, its members, its member associations and the entire African continent".
A CAF statement added that it would recommend that the executive committee "file a law suit, if necessary, so that the authors of this smearing and defamatory campaign against African football leaders are brought to book".
American lawyer Michael Garcia is currently heading an independent inquiry into the bidding process for both the 2018 World Cup, which will be staged in Russia, and the 2022 event in Qatar, and will deliver his findings to FIFA in mid-July.
Qatar's World Cup bid committee, meanwhile, is rejecting all allegations of wrongdoing and says it is confident the vote was won fairly.