McCarthy spoke about the Cowboys' gunslinger Wednesday at the NFL Scouting Combine in Indianapolis. Prescott, 26, is set to become an unrestricted free agent this off-season after playing on the final year of his contract in 2019.
The Cowboys also could place the franchise tag on Prescott before March 10, keeping him under contract for the 2020 season and out of the free agency market.
NFL free agency begins March 18.
The Cowboys have talked with Prescott about a long-term contract extension, but no agreement has been reached. McCarthy confirmed that Prescott still is the Cowboys' franchise quarterback despite his contract being in limbo. Prescott and McCarthy have been communicating privately during the process.
"What he's done [on the field] to this point speaks to itself," McCarthy said. "Really, Dak is in a business situation right now -- I've gone through this as a coach with a number of my players in the past.
"I think like anything, it's just time to be patient and let the business people work out the business matter. And that's really where we are as an organization. And that's where Dak is in his personal fight to get a contract done."
Prescott's contract has been just one of the lingering behind-the-scenes issues for the Cowboys over the last few seasons.
The Cowboys contractually locked up their offensive line and running back Ezekiel Elliott last off-season. In addition to Prescott, the Cowboys also want to bring back free agent wide receivers Amari Cooper and Randall Cobb next season. Linebacker Sean Lee and tight end Jason Witten also are on track to hit free agency.
The Cowboys hired McCarthy in January. He previously coached Cobb while both were with the Green Bay Packers.
"The goal is to have both of those guys back," McCarthy said of Cooper and Cobb. "[Cooper] did a lot of great things on tape and he really looks like he's in sync with Dak. I'd even say Randall even more. I was very impressed with Randall last year. He's [gotten] banged up a couple of years, but I thought he had a heck of a season. I was very impressed with him."
Prescott was selected in the fourth round of the 2016 NFL Draft. The Mississippi State product threw a career-high 30 touchdown passes and a career-high 4,902 yards in 16 starts in 2019. Prescott has never missed a start and has a 40-24 record as a starter.
He has a 1-2 record in three playoff appearances.
"I think he's gotten off to a great start," McCarthy said of Prescott. "He's built a really good foundation. I'm told he's a tremendous leader. According to my philosophy ... defenses get you to the championship, quarterbacks win championships. I definitively feel Dak is that quarterback."