Nonprofit colleges and universities may be failing to report the full extent of their taxable income to the IRS, according to Lois Lerner, the agency’s director of exempt organizations. The IRS found in a survey sent to 400 schools in October 2008 that about a third of the respondents aren’t filing forms detailing their taxable income even though many operate businesses unrelated to teaching and research. The survey led to the audit of Harvard University and more than 30 other colleges.

Those schools that do file never pay taxes because they claim losses that wipe out any profits, Lerner said the survey found. “We’re going to be looking at that in the audit to see how colleges and universities are allocating gains and losses,” Lerner said yesterday on a panel at the National Association of College and University Business Officers annual meeting in San Francisco.