The move to abandon the tradition at Anglia Ruskin University was described as "health and safety gone mad" by student organisations.
The university, which has campuses at Cambridge and Chelmsford, said the action had been taken because a mortar board had injured a graduating student several years ago.
The student had to be taken to hospital for stitches after he was struck in the face. The incident is the only mortar board inflicted injury to have been recorded by the university.
A statement on the university website said: "It is requested that graduates do not throw the hat up into the air, as this not only causes damage to the hats, but can also cause injury if the corner of the hat hits the graduate or others who may be nearby."
Frankie Whiffen, the Student Union President, branded the university authorities "anti-fun, health and safety killjoys" adding: "We support university policies but it sounds like health and safety gone mad.
"It's an important tradition, and who is going to go round stopping it anyway - the hat police?
"It's outrageous that decades of tradition should be shelved because big brother is worried a group of grown adults can't catch a hat properly."
He added: "It's ridiculous and puts a dampener on the graduates' big day."