The soccer federation most affected by the global corruption scandal that upended the sport more than a decade ago is under scrutiny again, just weeks before the World Cup.

Alejandro Dominguez, the leader of Conmebol, the South American soccer organization at the center of the sprawling FIFA scandal in 2015, is facing an ethics complaint that he received millions of dollars from the funds that had been recovered from that case. The complaint was made by a whistle-blower who claims to have direct knowledge of the payments.

Senior FIFA officials have been aware of the complaint against Mr. Dominguez to its ethics committee for more than a year, according to three people with direct knowledge of the complaint who spoke on the condition of anonymity because they were not authorized to discuss the matter.

Mr. Dominguez, one of the biggest power brokers in the sport, also serves as one of the eight vice presidents of FIFA. The complaint accuses him, along with another senior Conmebol official, of receiving more than $5 million from the money recovered by the soccer federation after it secured the return of millions of dollars lost to corruption schemes.

Conmebol, one of soccer’s six continental governing bodies, declined to comment, saying only that it was unaware of an ethics complaint. FIFA did not respond to repeated requests for comment. Mr. Dominguez did not reply to a request for comment.

The revelation of the complaint comes at a particularly sensitive time not only for Mr. Dominguez but also for FIFA, with the World Cup scheduled to begin next month in Mexico, Canada and the United States.

He took the helm of Conmebol, which represents 10 South American FIFA member nations, in 2016 after his predecessor was indicted and jailed as a result of the 2015 investigation.

Soccer fans worldwide were stunned after an investigation by the U.S. Department of Justice uncovered more than $150 million in bribes and kickbacks spanning two decades between soccer officials from two soccer federations — Conmebol and Concacaf, the governing body for North and Central American soccer — and sports marketing executives. Investigators said officials rigged World Cup bids and awarded broadcast and marketing contracts in exchange for bribes that were paid through convoluted financial deals or sometimes with briefcases full of cash.

The status of the complaint against Mr. Dominguez is not known. But there has been increased secrecy around FIFA’s complaints and investigations since Gianni Infantino took over as president in 2016. Before that, its ethics committee, ostensibly an independent body, would confirm details of cases that had been subject to investigations, particularly high-profile individuals. Last year, María Claudia Rojas, a Colombian who heads the adjudicatory arm of the ethics committee, told reporters that cases can take several years to reach a conclusion.

“There’s no transparency whatsoever in how the ethics committee handles complaints, and often no final resolution,” said Miguel Maduro, the first head of governance appointed by Mr. Infantino. “Instead of dismissing the complaint or acting on it, they simply many times keep it there and no one knows what they will do.”

FIFA publishes an annual summary in which the details of ethics complaints received and actions taken are provided in an anonymized manner revealing little about specific cases.

According to the complaint against Mr. Dominguez, which was described to The New York Times in detail, the recovered money relates to funds retrieved from bank accounts that were once controlled by officials at Conmebol who were implicated in the 2015 scandal, in which more than a dozen South American soccer officials were indicted. The ethics complaint alleges that some of the money was kept by Mr. Dominguez as a form of secret bonus or commission, and by at least one other official at the confederation.

Documents reviewed by The Times show agreements between Conmebol and the family of its former president Nicolás Leoz, who had been among the officials indicted by U.S. authorities before his death in 2019. The documents reveal a complete settlement between the parties and a return of more than $50 million from accounts in Paraguay and Switzerland. The payments were designed to end any litigation and did not recognize any guilt, the documents showed. Conmebol in 2020 confirmed it had secured the money. Mr. Leoz died amid a legal effort to avoid extradition to the United States.

In 2020, after securing the return of the stolen funds, Mr. Dominguez said, “I made a promise to do justice beyond the judicial sphere, to renew the institution, to generate value beyond what was previously known and to reinvest that value, to give back to football what belongs to football.”

Since taking over the South American soccer federation, Mr. Dominguez has chaired committees responsible for the finances of its global governing body, FIFA, and until recently, he was also a member of a small panel that decided the millions of dollars in salary and benefits for Mr. Infantino. Mr. Dominguez also secured major FIFA events for Paraguay, including prestigious hosting rights to one of three games of the 2030 World Cup, which will be played in South America.

He has established himself as one of soccer’s most visible leaders, aggressively building a social media presence that includes a dedicated team of videographers who document him at major events. He has also used his platform to assert that Conmebol has moved on from its past and tout that it recovered the stolen funds. Upon his rise in the soccer establishment on his continent, Mr. Dominguez said he would introduce “control systems that help our accounts to be up-to-date and which will prevent any individual or private entity to profit over the interests of football.”

The federation was named as a victim in the 2015 case along with FIFA and Concacaf. That led to the federation being named in 2021 as one of the parties that could have access to $201 million in compensation from a specially created entity called the World Football Remission Fund with the Department of Justice.

“I am delighted to see that money, which was illegally siphoned out of football, is now coming back to be used for its proper purposes, as it should have been in the first place,” Mr. Infantino said when the fund was announced.

Since then, he has often said that FIFA has moved on “from a toxic organization at the time, to a highly esteemed and trusted global sports governing body.”

The structure of global soccer, however, remains largely the same as then, with the FIFA president sitting atop an organization that is answerable to its 211 member federations. Those members decide who will lead the organization every four years, and Mr. Infantino recently announced he would run for a final term next year.

In April, after a meeting of its executive council, Conmebol became the first of soccer’s regional bodies to back Mr. Infantino, who has now led FIFA for a decade, to continue in the post, even before he announced his intentions. Mr. Dominguez started his address that day by presenting Mr. Infantino with a captain’s armband.