Student loans in Northern Ireland were financed by England's Department for Education and Skills, an Audit Office report says.
The mistake happened because the Student Loans Company registered students in the west of the province as living in England.
The blunder emerged when the company found itself short of about £18.4 million of loans issued to students from Ulster two years ago.
The comptroller and auditor general's report said: "It would appear that these NI loans were funded by the DFES. An unknown amount of repayments has also been misallocated."
The province's Department of Education and Learning, whose locally elected minister, Carmel Hanna, is suspended with the rest of Northern Ireland's power-sharing administration, chose not to refund the DFES, which it is entitled to do under government accounting rules.
But the mainland department told the auditor it was discussing with the DEL how to handle any such issues in future.