Jones, speaking in the locker room following Sunday's 42-17 blowout loss to the Denver Broncos, called the ESPN report an "exaggeration."
"All of that is without any substance at all," Jones told reporters, per the Fort Worth Star-Telegram. "The exercise of looking and extending our commissioner's contract is one that we keep really in tight. There are certainly exaggerations there. That's not the way that works. I've always supported Roger and let's just leave it at that. I wouldn't get into the nuances and deny anything that was written, whether it was true or not."
Sources familiar with the contract talks told ESPN's Adam Schefter and Chris Mortensen earlier Sunday that Jones has slowed down, if not impeded, negotiations aimed at an extension for Goodell.
Jones also has interjected himself on to the NFL's six-man compensation committee, becoming the unofficial seventh member, according to ESPN.
Jones, who acknowledged his role in the process and referred to himself as an "ombudsman," addressed the perception his interest in Goodell's contract may be tied to the commissioner suspending star running back Ezekiel Elliott.
The NFL is currently in a court battle with Elliott, who remains eligible to play under an injunction despite the league's six-game suspension for alleged domestic violence.
"I could understand why ironically we've got the Zeke issue at the same time that we're looking at extending Roger's contract, that he made the ruling," Jones said. "I see that. But every day I deal with conflicts of interest and he deals with it, the commissioner deals with it every day. You just have to get used to that. You look at the issue as the issue."
Goodell's current deal as commissioner expires in 2019, and it was reported last month that he and the NFL were close to a new five-year extension that would run through the 2024 season.
Jones was asked if it was Goodell who told him Elliott was not going to be suspended.
"I wouldn't dare get into any of our conversations or anything," Jones said. "But we did have conversations regarding Zeke."
The 58-year-old Goodell succeeded Paul Tagliabue in September 2006. Goodell made nearly $32 million in fiscal year 2015, according to the league's tax filing from that year, and has made $212.5 million in his first 10 years as commissioner. The NFL is no longer required to file his salary as the league office has given up its non-profit status, thus salary figures are no longer available.
Goodell first joined the league as an intern in 1982, working his way up the executive ladder. He was appointed executive vice president and chief operating officer by Tagliabue in 2001. Five years later, Goodell succeeded Tagliabue.
The NFL's collective bargaining agreement is set to expire after the 2020 season, and NFL Players Association executive director DeMaurice Smith said last month he believes there will be a work stoppage in 2021.
Since the agreement was signed, the players union has clashed with Goodell and the league in notable cases such as Elliott's suspension, Tom Brady's Deflategate suspension and Adrian Peterson's suspension for child abuse.