Trinity College Dublin is writing to current and former students to try and recoup €1.7m in fees.
Just over 500 students were accidentally undercharged registration fees over the past three years due to an administrative oversight.
It affects those who applied for a Student Universal Support Ireland grant, or SUSI.
They were not approved for the grant, but were mistakenly charged lower fees as if they had been.
In a statement, TCD said: "It can sometimes take a long time for these decisions to be reconciled with the university's student record system.
"For the past three years, the college has mistakenly believed it was owed money by SUSI.
"In fact, the money was owed by individual students and that money is now being recouped."
It added that around 80% of students owe €3,000 or less - but a "small number" are being asked to pay up to €9,000.
SUSI processed more than 103,000 applications in 2017 - with over 81,000 students awarded a grant.