Ulster University spent £226,000 on settlements that included "gagging clauses" for staff in 2017.
The university said the amount related to six settlements, which included non-disclosure agreements (NDAs).
Queen's University in Belfast refused to disclose if it had made any settlements on a similar basis.
Figures obtained by the BBC had shown that 96 UK universities - including Ulster University - spent about £87m on pay-offs with NDAs since 2017.
NDAs are designed to stop staff sharing trade secrets if they changed jobs but there are allegations that they are sometimes misused to protect serial perpetrators of misconduct.
Many of the universities told the BBC they were unable to disclose why the agreements were signed, so it is unclear how many relate to allegations of bullying, harassment or sexual misconduct.
In a statement to BBC News NI, Ulster University said it used non-disclosure agreements "in appropriate circumstances including where there is a requirement to retain and protect the confidentiality of commercially sensitive information".
It added: "Negotiated settlements of this kind are mutually confidential for both parties and as these are in low numbers in a relatively small local market, provision of amounts may identify individuals or personal information, which would breach our confidentiality obligations."
'A small number of agreements'
Queen's University told BBC News NI that NDAs are widely used across the higher education sector but it refused to disclose if it has used any since 2017.
"Disclosure of information relating to settlements or agreements that have included confidentiality clauses would negatively impact on the university's ability to negotiate settlements and agreements in a robust and responsible manner in the future," it said.
"In addition, due to the small number of agreements, disclosure of the details requested would risk breaching the confidential nature of these agreements as it may be possible to identify the details of individual settlements."
Universities UK, which represents 136 higher education institutions, said that universities used NDAs for many purposes.
"However, we also expect senior leaders to make it clear that the use of confidentiality clauses to prevent victims from speaking out will not be tolerated," it said.