The 77-year-old billionaire, a friend of President Donald Trump, was charged in connection with an investigation into an illegal massage parlor operation, police in Jupiter, Florida, said.
Kraft, whose club recently beat the Los Angeles Rams for its third title in five seasons, is among 25 men charged with solicitation, said police chief Daniel Kerr, adding that video evidence had been collected in raids made over recent days.
"We're as deeply stunned as anyone else," Kerr added.
A spokesperson for Kraft denied that the tycoon had "engaged in any illegal activity" but declined to comment further.
Kraft has not yet been arrested on the two misdemeanor charges for each of his alleged visits to the Orchids of Asia day spa. About 200 arrest warrants have been issued, police said, with more expected.
The charges were made as part of an eight-month investigation into human trafficking that included surveillance in five spas and shutting down 10 in a case prosecutors say has links to China and New York.
Police say Kraft, who does not face trafficking charges, was twice driven to the spa and that they have video evidence of him paying for a sex act and of sex acts with a prostitute.
While uncertain of the amounts Kraft actually paid, police said the average fees for services at the parlor ranged from $59 for 30 minutes to $79 for one hour.
Kraft has a net worth of $6.6 billion, according to Forbes magazine, putting him among the top 20 percent of the Forbes 400 richest list for 2018.
Kraft has been a frequent visitor to Trump's Mar-a-Lago estate in Florida, with the president tweeting his congratulations to the Patriots - including Kraft, quarterback Tom Brady and coach Bill Belichick by name - for reaching the Super Bowl and after past championships.
Belichick and Kraft were among the Patriots delegation that visited Trump in the White House in 2017 after their Super Bowl victory over Atlanta.
Kraft handed Trump a personalised Patriots jersey during the visit.
Asked by reporters at the White House on Friday about the charges against Kraft, Trump said "it's very sad."
"I was very surprised to see it," Trump added. "He's proclaimed his innocence totally. I'm very surprised to see it."
Kraft, whose wife, Myra died in 2011, became the principal owner of the Patriots in 1994 and has seen the club win six NFL crowns in all.
Punishment from the NFL could be forthcoming if Kraft is found guilty. A league bylaw gives NFL commissioner Roger Goodell the power to sanction an owner for "conduct detrimental to the welfare of the league."
"The NFL is aware of the ongoing law enforcement matter and will continue to monitor developments," the league said in a statement.
Personal conduct policies are stricter on NFL owners and league employees, as Indianapolis Colts owner Jim Irsay found in 2014 when he was suspended for six games and fined $500 000 after being arrested on drug charges.
Kraft's sports holdings also include Major League Soccer's New England Revolution, a share of a mixed martial arts promotion group and a team in the videogaming e-Sports Overwatch league.
Women, some of them from China, lived in the spa and were not allowed to leave, according to Will Snyder, sheriff of Martin County. Some women averaged as many as eight clients a day, police said.