Most are seeking asylum and have been granted temporary bridging visas while their cases are processed.
But 50 have made no formal application for permission to stay.
Mr Dutton has warned they will be found and deported.
A week-long guessing game over the number of Commonwealth Games athletes and officials still in Australia after their visas expired a week ago has finally ended.
Home Affairs Minister Peter Dutton previously refused to say, but the deputy secretary of his department, Malisa Golightly, has revealed the figures in a Senate Estimates hearing.