The Prime Minister last week made a plea to the English, Welsh and Northern Irish to urge Scots to reject independence in September's referendum.
Speaking at the velodrome in London's Olympic Park, he summoned up images of Scot Sir Chris Hoy winning a record medal haul for Team GB while standing above a Glasgow Caledonian logo.
The university's Combined Union Committee said: "As a public body the University must take a sensitive and neutral position. It is wrong that the university senior management allowed the GCU's image to be used in this way by the PM."
The union added the university court was only told of the event the day before and it was promoted as a business event.
A spokeswoman last night insisted the university remained neutral in the independence debate.