N.F.L. Commissioner Roger Goodell’s pay for the past two fiscal years totaled almost $128 million, bolstered by bonuses for helping the league’s owners clinch a new 10-year labor deal with the players and secure media contracts worth more than $100 billion over the next decade.

The nine-figure combination of salary, bonuses and other benefits made Goodell one of the highest-paid executives in the country, and the disclosure of the deal comes at a time when he has been criticized for his handling of numerous thorny issues, including the investigation into widespread workplace harassment at the Washington Football Team.

Goodell’s compensation was discussed at a two-day meeting of the league’s owners in Manhattan this week. During a session on Wednesday when only team owners were in attendance, a slide was shown listing the commissioner’s pay: $63,900,050 per year, or just under $128 million for the fiscal years 2019-20 and 2020-21.

The N.F.L.’s calendar year begins in mid-March, and Goodell’s pay each year is determined by several prominent committees made up of owners of the league’s 32 clubs.

The owners on Wednesday were told that Goodell’s recent pay package, about 90 percent of which is bonuses, was so large because he had helped secure such favorable labor and media deals, according to four people who attended the meeting and spoke on the condition of anonymity because it was a private session among about two dozen team owners.

The N.F.L. declined to comment.

In the past, the compensation committee recommended a figure that went to the full ownership for approval. But after a dispute between the Dallas Cowboys owner Jerry Jones and the half-dozen team owners who made up the compensation committee, Goodell’s contract was restructured to rely heavily on performance-based bonuses instead of guaranteed salaries.

In 2017 Goodell signed a five-year deal that took effect in 2019 and is worth up to $200 million in total, much of it tied to his meeting financial and nonfinancial goals for the league. The owners on three influential committees, which have a total of about 20 members, decide annually whether the commissioner has met the targets.

The labor deal, which the players narrowly agreed to pass just as the coronavirus pandemic began in March 2020, added a 17th regular season game to the calendar. The stability guaranteed by a new collective bargaining agreement also helped the N.F.L. negotiate far larger television contracts with CBS, Fox, NBC and other outlets. Goodell also steered the league through the pandemic, with no games canceled during the 2020 season.

While Goodell is often criticized by the news media, fans, politicians and supporters of women’s rights, the league’s owners by and large support him, even as they quietly acknowledge that he is hardly the perfect leader for North America’s most successful professional sports league.

His tenure as commissioner, which began in 2006, has been punctuated by controversies and self-inflicted problems, including his handling of cases involving domestic violence, bullying and players’ protesting police brutality and inequality during the national anthem.

Goodell has also angered teams that he has penalized, most notably when he suspended star players like Tom Brady and Ezekiel Elliott. But owners understand that Goodell’s strengths help make them money, and that his institutional knowledge would be hard to replace.

Several owners said in 2017 that Goodell had told them that he would step down after his current contract ends in 2024. He may be willing to stay beyond that date, according to some media reports.

Goodell, 62, has worked at the league for nearly four decades, and has known and is known by many owners, their ancestors and their progeny. He is friendly with the leaders of the league’s broadcast partners, whose rights payments make up about half of the N.F.L.’s annual revenue, which has more than doubled since Goodell took over in 2006.

In 2010, Goodell said he wanted revenue to hit $25 billion by 2027, and thanks to the new media deals, the league appears on pace to meet that target.

For years, Goodell’s compensation, along with that of other top league officials, was included in annual filings that had to be published because the league office (unlike the teams) was a tax-exempt organization. In 2015, the league dropped its decades-old tax-exempt status after critics, including some members of Congress, argued that the government was losing millions of dollars in potential revenue.

As a result, the league no longer has to publicly disclose its tax returns, which included the salaries of its five highest-paid executives. Major League Baseball took a similar step several years before the N.F.L. By and large, awkward questions from the news media about the commissioner’s pay package disappeared.