Customs and Excise will investigate Cambridge University's accounts after a spot check uncovered "incorrect" applications for tax relief worth Pounds 20,000.
HM Customs allows VAT relief worth "millions, if not hundreds of millions of pounds" on goods bought by the higher education sector for medical research, diagnosis and treatment, said a spokesman.
A memo sent by Cambridge's finance division to departmental accounting staff last month said: "A recent examination by HM Customs and Excise Officers of the accounting records at a sample of university departments has highlighted a number of instances where certificates have been incorrectly issued in order to obtain the reliefI HM Customs and Excise intends to conduct a more comprehensive inspection of such records and will, if appropriate, visit university departments to examine the information."
A Customs spokesman would not discuss individual cases but said: "If we find that an institution is not accounting for its VAT correctly, we may want to look at the accounts in a wider sense."
Cambridge treasurer Joanna Womack said: "A VAT investigation of a supplier threw up a small number of cases where VAT certificates had been wrongly issued. We will make a refund. It is a small amount of money and an extremely minor incident."