The 79-year-old Blatter was re-elected to a fifth term on Friday, two days after a corruption crisis erupted and seven soccer officials were arrested in Zurich ahead of the FIFA congress.
"This mandate does not seem to be supported by everybody in the world of football," Blatter said Tuesday at a hastily arranged news conference. "FIFA needs a profound restructuring."
Elections are expected to take place sometime between December and March.
"I will continue to exercise my function (until the new election)," Blatter said.
Blatter said he reached the decision after he "thoroughly considered my presidency and ... (about) the last 40 years in my life."
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