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The Hattiesburg American reports that the department predicts a shortfall of at least $1 million for 2012-13.
But interim Southern Miss President Aubrey Lucas said measures taken by the university and the athletic department whittled about $800,000 from the projected debt in 2011-12. He says steps are in the works to end the red ink.
Those include scheduling road games for large, guaranteed paychecks.
State College Board policy forbids universities to finish a fiscal year in the red.
Lucas says audits had forecast a $1.2 million deficit for the 2011-12 fiscal year, but USM pared that down to less than $400,000.