Under a federal statute called the Equity in Athletics Disclosure Act, colleges and universities must report to the government the number of male and female athletes participating in each sport they offer. Separately, the NCAA also requires that information as a condition for membership. Both the government and the NCAA are asking for the same information, but as USA Today reports today, institutions frequently report different numbers to each.
Sometimes schools count don't count athletes who have already been counted as participants in other varsity sports, even though both the government and the NCAA want to know the total number of participation opportunities rather than the number of individuals taking part. One compliance officer admitted to accidentally counting practice players for one source and not the other. Another source of error occurs in tallying up the gender breakdown of the general student body, the denominator in a proportionality calculation. Depending on who in the university is doing the counting, different definitions of "full time undergraduate" might be used.
The paper also quoted the president of the College Sports Council that these disparities support its position that Title IX hurts men's sports, a claim that contravenes data derived from government sources. But the USA Today researchers who looked at both government and NCAA data for all public Division I schools say that when there are disparities (which was the case for 53 of 96 schools), about half the time the NCAA data paints a better compliance picture, and half the time, the government data does. Based on this, I don't think that using one source or other can generate a political advantage.