In the August 6, 2006 issue of West, the Sunday magazine of the Los Angeles Times, an article by Claire Hoffman followed Francis across the country.[15] In it, Hoffman bore witness to Francis' numerous alleged illegal activities, including habitual supply of alcohol to underage girls. Hoffman reported Francis' alleged rape of an 18 year old. Quoting the alleged victim, who was under the legal drinking age in the USA and had allegedly been supplied alcohol by Francis and his entourage, Hoffman wrote, "Eventually, [she] says, Francis told the cameraman to leave and pushed her back on the bed, undid his jeans and climbed on top of her. 'I told him it hurt, and he kept doing it. And I keep telling him it hurts. I said, 'No' twice in the beginning, and during I started saying, 'Oh, my god, it hurts.' I kept telling him it hurt, but he kept going, and he said he was sorry but kissed me so I wouldn't keep talking.'" Then, she says, he opened the door and told the cameraman to come back, saying, "She's not a virgin anymore." She says she's haunted by that night. After the report was published, Francis and his lawyer issued contradictory statements, Francis denying that he engaged in sexual intercourse with the alleged victim, while his lawyer claimed that intercourse had occurred consensually. Hoffman also reported that she herself was assaulted and "humiliated" physically by Francis in front of his cheering entourage, stating that "the pressure he applied was so intense that hours later, my arms were covered in red hand marks".

Francis was arrested at the Panama City-Bay County International Airport on April 10, 2007 for violating a contempt of court citation during negotiations in a civil lawsuit brought by seven women who were underage when they were filmed by his company on Panama City Beach during spring break in 2003.

Lawyers for the women disclosed to U.S. District Judge Richard Smoak that Francis became belligerent throughout the settlement talks, shouting profanities and threatening to "bury them." Smoak ordered Francis to settle the case or go to jail; subsequent negotiations were mediated, but broke down, inciting Smoak to issue a contempt of court warrant. The 11th U.S. Circuit Court of Appeals in Atlanta refused to let him remain free pending an appeal.[34].

Francis was sentenced to 35 days in jail for contempt of court.[35] On May 15, 2007, Judge Smoak ruled that Francis will be sent to Nevada to next face charges of federal tax evasion.[36]

The Associated Press (AP) reports that on Thursday, April 12, 2007, Francis was charged with bribery, possession of a controlled substance, and introducing contraband (cash and drugs) into the Panama City, Florida jail. The AP reports that Francis (in jail for contempt of court) unsuccessfully offered a guard one hundred, and then five hundred dollars, for a bottled water. Jailers allegedly found drugs including Lunesta and lorazepam in the jail cell. Francis reportedly faces up to five years in prison if convicted on these charges.[37] The AP indicates that The News Herald of Panama City reports Francis left the court room crying as he was led back to his cell, telling his parents "I didn't do anything" as he was led away.[38] A psychiatrist hired by Francis' defense team stated in his report that Francis demonstrates "significant psychiatric issues" and did "express a potential for suicidal activity if his incarceration is prolonged."[39]

On April 11, 2007, Francis was indicted by a federal grand jury in Reno, Nevada on two counts of tax evasion[40][41] under 26 U.S.C. § 7201[42]

Francis is charged with filing with the Internal Revenue Service a false and fraudulent Form 1120S, U.S. Income Tax Return for an S Corporation, for Sands Media, Inc. (a company for which Francis allegedly is the sole shareholder, president and chief executive officer), for the year 2002. The indictment charges that the return overstated deductions, including $3,784,390 for construction of a residence in Punta Mita, Mexico, as a false consulting services expense; a false $500,000 insurance expense; and an additional $10,411,020 in false consulting services expenses.[43] The indictment also charges that Francis understated his income on his own 2002 Form 1040, U.S. Individual Income Tax Return.[44] The indictment also charges various violations for the year 2003, including an allegedly false insurance expense deduction of $1,666,666.67 on the 2003 Form 1120S return for Mantra Films, Inc., a company for which he allegedly is the sole shareholder, president and chief executive officer.[45] In a press release, the United States Department of Justice asserts that the false business deductions total over 20 million dollars.[46]

The Los Angeles Times has quoted his attorney, Jan L. Handzlik, as saying: "The government has chosen to make a criminal case out of what we believe to be, at most, a civil tax dispute [...] We are also disappointed about the timing of these charges in light of Joe's difficulties in Florida. This is turning into a litigation dog pile."[40] If convicted, Francis could face up to ten years in prison and substantial fines. The trial is set to begin on October 2, 2007.[47]

On April 25, 2007 in Los Angeles, Joe Francis was charged with a misdemeanor of sexual battery for allegedly touching an 18-year-old woman repeatedly on her breasts, buttocks and thighs in spite of her protests. The incident is alleged to have occurred at a restaurant in January 2007.[48]