FIFA has asked Swiss prosecutors to investigate possible criminal offences committed by individuals involved in the 2018 and 2022 World Cup bidding processes.
A statement from world football's governing body said Eckert had found grounds to suspect individuals involved in the process of illegally transferring assets "with connections to Switzerland".
It read: "Judge Eckert has recommended that a criminal complaint be lodged with the office of the Attorney General of Switzerland in Bern.
"This criminal complaint has been lodged today.
"The subject of the criminal complaint is the possible misconduct of individual persons in connection with the awarding of the hosting rights of the 2018 and 2022 World Cups.
"In particular there seem to be grounds for suspicion that, in isolated cases, international transfers of assets with connections to Switzerland took place, which merit examination by the criminal prosecution authorities.
"Unlike FIFA's bodies, the Swiss criminal prosecution authorities have the ability to conduct investigations under application of criminal procedural coercive measures."
Blatter said the move shows FIFA, which has faced an abundance of allegations over corruption, is not opposed to transparency.
He added: "If we had anything to hide, we would hardly be taking this matter to the office of the Attorney General."
The Swiss also said there would be "no change to Judge Eckert's statement that the investigation into the bidding process for the 2018 and 2022 FIFA World Cups is concluded."
FIFA's ethics investigator Michael Garcia filed a 350-page report into the bidding campaigns in September but claimed Eckert's shortened summary contained "numerous materially incomplete and erroneous representations of the facts and conclusions".
Eckert denies misrepresenting Garcia's report and is due to meet with the United States attorney to discuss the issue on Thursday (November 20).
"My statement was based on the Garcia report," he said.
"I can only work with the material contained in it, and in my view, there was insufficient clear evidence of illegal or irregular conduct that would call into question the integrity of the award process as a whole.
"However, in certain places, the report does indicate that further clarification is needed of certain circumstances.
"Much of this clarification work can be carried out by the FIFA Ethics Committee itself, while the remainder is the responsibility of the relevant national investigatory authorities."
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