A third-year student raised the alarm after she discovered a tiny hole in a condom obtained from her college's welfare officer.
After checking the remaining condoms in the box she found that half had been pierced with a fine needle.
Some students have already started blaming the university's religious groups for the sabotage.
The student, from Newnham College, said the potential consequences of someone damaging condoms didn't 'bear thinking about'.
She said: 'I only noticed the hole when I threw the condom wrapper away. You could actually see daylight through it.
'Who the hell would do such a thing? And how would they feel if their actions led to someone contracting HIV? It doesn't bear thinking about.'
The condoms had been bought by the college welfare officer from Cambridge University Students' Union (CUSU) just an hour before the student discovered the sabotage.
The condoms, which are routinely distributed by the union to colleges, had been stored in unsealed boxes in an unlocked cupboard in the union's office.
There are now fears that saboteurs could have attacked condom supplies stored in up to 20 other Cambridge colleges.
Two years ago, similar attacks at King's College were attributed to the Cambridge Pro-Life Society, claims the president of the society strongly denied at the time.
Current Cambridge Pro-Life Society President Sam Corio, 26, has distanced her group from the controversy, condemning the attacks.
The Queens' college economics student said: 'Sabotaged condoms expose their users to life-threatening STIs.
'Because they increase the probability of unplanned pregnancies damaged condoms also potentially contribute to the loss of unborn human lives.'
This is not the first time Cambridge University has faced controversy over the quality of condoms issued to students.
In October 2008 the Cambridge Union Society handed out more than 1000 condoms branded with the debating group's logo at the freshers' fair.
The Union insisted that the condoms came from an NHS supplier and met European and British safety standards.
But CUSU sent an email to all colleges warning that the condoms were unsafe after spotting that they did not have a kitemark indicating British Standards Institution approval.