The newspaper found schools counted athletes who no longer wanted to compete or never played for that team, listing male practice players as women and trimming the rosters of men's teams.
The Times analyzed public records from more than 20 colleges and universities and federal participation statistics from all 345 institutions at the NCAA's highest level.
"Those of us in the business know that universities have been end-running Title IX for a long time, and they do it until they get caught," University of Miami President Donna Shalala told the paper.
National champion Texas A&M and Duke are among the elite women's basketball teams that take advantage of a federal loophole that allows them to report male practice players as female participants, the report said.
Women have grown to 53 percent of the student body at Division I schools, yet make up 46 percent of all athletes.
Instead of putting money into new women's teams or trimming the rosters of football, which can have 111 players, some schools are engaging in "roster management," the Times said. Shrinking budgets can prompt such an approach.
"It's easier to add more people on a roster than it is to start a new sport," said Jake Crouthamel, a former Syracuse athletic director.