Multiple media outlets reported that alcohol was found in Jones' system when he took a random drug test as part of a plea agreement that resolved his cocaine possession charge in July. He was charged with contempt of court.
Jones was given a choice of serving 10 days in jail or entering a six-week residential treatment program, The Florida Times-Union reported. He at first opted for the treatment program, but Judge Mary Ann Gunn suggested he think about what a prolonged stay in treatment would do to his NFL career. Jones then changed his mind.
"Many of the reports surrounding today are extremely inaccurate," Jones' agent, Dave Butz, said in a statement. "First, Matt was not charged with possession of any controlled substance. The judge went on the record today saying that Matt has been respectful and very compliant throughout his time in the program.
"The only issue today is that Matt admitted to the court that he drank a couple of beers while playing golf last week with a friend. I had a very positive conversation with the prosecuting attorney this evening in which she was adamant that 'this is not a new charge.'"
Jones tested positive for alcohol on Feb. 27 and appeared in court on Monday and admitted using alcohol during a golf outing the day before the test. He was arrested and the judge set his bond at $150,000.
Monday's arrest, confirmed to ESPN.com by deputy R. Hatcher of the Washington County police department, came at 6:21 p.m. in the same county in which Jones was arrested last year.
"We're aware of the situation and are still gathering information," said Jaguars general manager Gene Smith, according to The Florida Times-Union.
Jones was the Jaguars' leading receiver with 65 catches and 761 yards despite the suspension under the league's personal conduct policy. That suspension came after a failed appeal and was the result of a violation of the league's substance abuse policy.
Jones was arrested and charged with one count of cocaine possession on July 10, 2008, when a Fayetteville police officer saw him inside a parked car allegedly cutting up cocaine with a credit card. The charge carried a maximum sentence of 10 years in prison and a $10,000 fine. Jones pleaded not guilty and later reached agreement with prosecutor John Threet's office to send the case to drug court.
On Oct. 13, a judge accepted Jones into a drug treatment program that could erase the felony cocaine charge against the former Arkansas star. The former Razorbacks quarterback was ordered to participate in NFL-sponsored substance-abuse counseling and random drug testing through the end of the football season, then return to Fayetteville to complete the intervention program, Gunn said.
Gunn, who presides over the Washington County Drug Court, said at the time Jones could be bounced from the program if he failed a drug test or missed a counseling session. Jones said in court that he was "very committed" to completing the program and said he had passed random NFL-administered drug tests since his July 10 arrest.
The quarterback-turned-wide receiver stood with his parents in Gunn's courtroom, which was filled with drug offenders and treatment program graduates. He said he wanted to enter Gunn's program because "I want to make sure it doesn't happen again."
Monday's arrest could affect his agreement on last year's charge and also lead to further penalties from the NFL.
Lisa Dennis, a deputy prosecuting attorney for the drug court, told the Times-Union that Jones had complied with the program and was frank with the judge about the alcohol violation.
"But the judge wanted to emphasize that even having a beer is against the rules," Dennis told the newspaper. "It's not a terrible infraction, but he broke a rule."
Information from ESPN.com's Paul Kuharsky and The Associated Press was used in this report.