Add one more strain to the finances of U.S. universities: a decline in enrollment.

Last week the U.S. Census reported college enrollment declined for the first time in six years in the fall of 2012. That, in turn, threatens higher education revenue, said Moody's Investors Service in a special report on Monday.

Already, "precipitous enrollment declines for fall 2013" have hurt the credit quality of two private colleges—Loyola University in Louisiana and Central College in Iowa—and a public one, St. Mary's College in Maryland.

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"Enrollment declines in higher education are credit negative because they heighten competitive pressure for all universities. This limits opportunity to grow tuition revenue, now the primary revenue for the majority of public and private universities," said Moody's.