A former athletic trainer at San Jose State University was accused Thursday of violating the civil rights of four women he was supposed to be treating for injuries.In a court filing on Thursday, the Justice Department charged Scott Shaw, the former trainer, of six counts of deprivation of civil rights under color of law, misdemeanors that together carry a maximum sentence of six years in prison and $600,000 in fines.The charges, brought in the United States District Court in San Jose, Calif., were announced less than a year after San Jose State agreed to pay about $3.3 million to 15 women who accused Shaw of wrongdoing. But the misconduct detailed in the federal charges, which prosecutors said occurred between 2017 and 2020, took place years after San Jose State first learned of concerns about Shaw’s behavior toward women under his care.In 2009, the university’s swimming and diving coach reported that athletes had complained of inappropriate touching by Shaw during physical therapy sessions. By the middle of the following year, a university investigator had accepted Shaw’s explanation that the touching amounted to pressure-point therapy, a widely used treatment technique. The matter was essentially closed.A revived inquiry, prompted by fears that the initial review had been insufficient and by the submission of information to the N.C.A.A. and the Mountain West Conference, began in 2019 and eventually substantiated accusations against Shaw by 10 athletes, including two who were then enrolled at San Jose State. An outside doctor who was consulted as part of that investigation said there was “no explanation or documentation available that there was therapeutic justification” for the techniques Shaw claimed to be using with the women.The university later reached a settlement with the Justice Department, which had concluded that the school had failed to comply with Title IX, a federal law that forbids discrimination on the basis of sex, including sexual harassment.All told, the investigations of recent years found that Shaw had inappropriately touched at least 23 women. Shaw resigned from the university, which also saw its president and athletic director leave after the accusations against the trainer came into public view, in 2020. A lawyer who has represented him did not immediately respond to a request for comment on Thursday.Thursday’s court filing said little about the trainer’s suspected criminal wrongdoing beyond that he had touched the breasts and buttocks of the women without their consent. The conduct, the Justice Department wrote, deprived the women “of liberty without due process of law, which includes the right to bodily integrity.”Shaw is far from the first medical staff member accused of mistreating or abusing athletes. The University of Michigan said in January that it had agreed to pay $490 million to more than 1,000 people who had been abused by a doctor, and Michigan State University reached a $500 million settlement in 2018 to compensate victims of Lawrence G. Nassar, a doctor.