Hartpury College in Gloucestershire returned the money to the agricultural national training organisation Lantra following an inquiry by independent auditors.
The college's director of enterprise Nick Robin was suspended and subsequently resigned.
The investigation was launched after beekeeper and course tutor Tony Boonham blew the whistle when he discovered false invoices relating to the hire of bee hives.
One invoice was for pound;12,480 and another was for pound;2,800. "It was completely news to me when I saw this," he said. "We already had all these hives."
Mr Boonham, who has since retired on grounds of ill health, passed his findings to Diana Organ, Forest of Dean MP. In a joit statement, Hartpury College and Lantra said the college has now repaid pound;31,858 which was incorrectly claimed.
Ms Organ alerted Lantra "concerning documentation which a senior member of college staff had used in support of the match funding element of an ESF claim relating to 1995." The college suspended its director of enterprise "on the grounds that there appeared to be evidence to support a charge of gross misconduct arising from falsification of documentation in support of a claim for grant funding."
Following investigations, the college's audit committee concluded that "one senior manager had been solely responsible for the falsification of the documentation".
Gloucestershire police were notified, but no action was taken.
A spokeswoman for Hartpury College refused further comment.