Universities have spent nearly £90 million on pay-offs with so-called gagging orders attached over the last two years, it has been reported.
The huge sum is said to have been spent on around 4,000 settlements, some of which are reported to relate to allegations of bullying, harassment or sexual misconduct.
Universities UK (UUK), the sector's representative organisation, said non-disclosure agreements (NDAs) were used for "many purposes", including protecting valuable research.
However, the body said the contracts should not be used to prevent victims from speaking out and such practices "will not be tolerated".
Using Freedom of Information laws, nearly 140 universities were asked by the BBC to detail how much they had paid in settlements that included NDAs.
Figures from the 96 institutions that responded showed around £87 million had been spent since 2017.
It was reported that NDAs were being used to silence allegations of bullying, harassment and sexual misconduct.
A UUK spokesperson said."All staff and students are entitled to a safe experience at university and all universities have a duty to ensure this outcome."
The body said it is developing comprehensive new guidance on sexual misconduct that will be published in the autumn.
The guidelines will cover NDAs, while UUK is also working with a government consultation on the issue.
The body added: "It's important to note that a confidentiality clause will usually be one part of a wider settlement agreement that has been negotiated between two parties and, crucially, the signing of an agreement containing such a clause does not prevent staff or students from reporting criminal acts to the police or regulatory bodies, or from making a disclosure under the Public Interest Disclosure Act 1998."
Chief executive of the Equality and Human Rights Commission Rebecca Hilsenrath told BBC Radio 4's Today programme: "I'm very disappointed by what I'm hearing, but not surprised because we've seen that this sort of behaviour is rife across all sectors and I'm afraid we're seeing a growing use of NDAs.
"There's a total legitimacy to use NDAs to protect commercial interests, (intellectual) property; they should not be used to stifle victims and to continue a culture of bullying."