Middleton also made contact with the IRD and was told he could dispute the loan.
The Herald on Sunday spoke to AMES principal Vic Sergeant, who said the procedures were stipulated by the New Zealand Qualifications Authority.
"We follow the rules as they were in 2004. We are updating our handbook at the moment and I can't comment on any particular case."
He did not know the academy's policy on the timeframe students would be able to leave the course without incurring the full cost.
NZQA chief executive Karen Poutasi said the stance at AMES contravened the fee protection aspect of the Education Act 1989: "It doesn't matter if the handbook was from 2004 or 2012, as the refund provisions were passed into law in 2000."
StudyLink, which administers the loans, said Middleton withdrew from studies within the timeframe to avoid paying the loan but said he had called back and changed his mind.
Middleton said he would appeal against the IRD decision.
Loan arranger
The number of student loan applications was up this year compared to last year by 8000 applications.
Head of StudyLink Susan Kosmala said it received 6000 calls a day and 97 per cent of applications were made online.