Michael Garcia cited a "lack of leadership" at the top of FIFA in a resignation statement. He also said he has lost confidence in the independence of his ethics committee colleague, German judge Joachim Eckert.
Though Garcia did not identify Sepp Blatter by name, he also revealed that the FIFA executive committee — led by the longtime president — made a failed complaint of unethical conduct against the former U.S. Attorney in September.
Speaking at the Club World Cup in Marrakech, Morocco, Blatter told The Associated Press he was stunned by Garcia's decision to resign.
"I'm just surprised," Blatter said. "It's all what I can say. Just that."
Garcia quit a day after the FIFA appeals panel rejected his challenge of Eckert's summary of the confidential 430-page investigation dossier. Last month, Eckert moved to close the case on the World Cup bidding contest because of lack of evidence.
Russia won the right to host the 2018 World Cup and Qatar was awarded the 2022 tournament.
After Eckert's summary was made public, Garcia claimed that the German judge had misrepresented his work and then launched his failed appeal.
"(My) report identified serious and wide-ranging issues with the bidding and (World Cup host) selection process," Garcia wrote Wednesday, adding that Eckert's decision "made me lose confidence in the independence of the Adjudicatory Chamber, (but) it is the lack of leadership on these issues within FIFA that leads me to conclude that my role in this process is at an end."
In his resignation statement, Garcia also questioned how FIFA can truly change after years of scandals and criticism.
"No independent governance committee, investigator, or arbitration panel can change the culture of an organization," Garcia wrote.
Garcia also revealed that the executive committee tried to have disciplinary proceedings opened against him for "allegedly violating the Code of Ethics through my public comments." The attempt was rejected by the chairman of the FIFA disciplinary panel, at a time when Garcia pressed for publication of key details from his report.
FIFA vice-president Michel Platini, also the UEFA president, called Wednesday's events "a new failure for FIFA."
"FIFA's ethics committee was created to increase transparency at the organization, that's what we wanted, but in the end it has just caused more confusion," Platini, the former France great who has refused to back Blatter for re-election but will not stand himself in the May 29 vote.
Garcia won support from Congress, with Sen. Bob Casey, describing his resignation as "understandable following repeated obstruction from FIFA" and calling for full release of the investigation report.
"Michael Garcia was a strong voice for accountability and transparency in an organization famously lacking either," said Casey, who has criticized Qatar's labour policies and treatment of migrant workers.
Garcia was appointed in July 2012 with the priority of probing the controversial 2018-2022 bidding contests. The investigation has helped reveal how willing Blatter's organization has been to confront some of its deep-rooted problems.
"For the first two years ... I felt that the ethics committee was making real progress in advancing ethics enforcement at FIFA," Garcia wrote. "In recent months, that changed."
FIFA said it would appoint an interim replacement for Garcia before electing a new ethics prosecutor in Zurich next May.
Since Garcia and his investigation team submitted their work in early September, clear splits emerged between the prosecutor and the judge. Eckert has seemed closer to FIFA in his approach and belief in how the ethics panel could use its powers, much to Garcia's increasingly obvious frustration.
Their working relationship was damaged by Eckert's 42-page report published by FIFA last month which suggested that the World Cup bidding probe should be closed for lack of strong evidence of wrongdoing.
"(W)hen viewed in the context of the report it purported to summarize, no principled approach could justify the Eckert Decision's edits, omissions, and additions," Garcia wrote.
Eckert said any corrupt and rule-breaking acts were of limited scope and did not influence the result of the December 2010 votes of the FIFA executive committee.
Still, with Garcia's work kept sealed against his wishes by strict FIFA Code of Ethics rules, critics and others have relied only on Eckert's word about the evidence against Russia, Qatar and the seven other bid candidates.
"It now appears that, at least for the foreseeable future, the Eckert Decision will stand as the final word on the 2018/2022 FIFA World Cup bidding process," Garcia wrote.
Garcia passed up the chance to stay and pursue his appeal against Eckert at the Court of Arbitration for Sport, which would likely take several months.
"I have concluded that such a course of action would not be practicable in this case," he said.
Still, prosecutions launched by Garcia against five senior football officials for alleged wrongdoing in the World Cup campaigns will continue. Those cases can be led by his ethics investigation deputy, Zurich-based former public prosecutor Cornel Borbely.
Germany great Franz Beckenbauer, a voting member of the FIFA executive committee in December 2010, is the highest profile of the five accused men.
Three current board members — FIFA vice-president Angel Maria Villar of Spain, Michel D'Hooghe of Belgium and Worawi Makudi of Thailand — also face sanctions for their actions during contests marred by claims of bribery, collusion and favour-seeking.
They are scheduled to attend a two-day executive committee session starting Thursday in Marrakech, Morocco.
On Friday, Blatter's ruling panel will discuss publishing all or parts of Garcia's file, and could finally see the document for themselves.
As part of Garcia-Eckert peace talks last month, they invited FIFA audit panel chairman Domenico Scala to analyze the investigation report. Scala can decide what the board should see before taking the next steps on a case that seems close to being shut down more than four years after the vote.
AP Sports Writer John Leicester in Marrakech, Morocco, contributed to this report.