The UCU union was unhappy that, during financial difficulties, some senior staff were rewarded financially, with the annual report document demonstrating the number of employees growing from 18 to 26 in a year.
"We are talking about substantial sums of money, which are enough to keep a great many of those who are facing losing their jobs in employment," said Mr Jones.
He said the union wanted to see fewer jobs with "very high salaries" to "protect jobs which command a lower salary, but which, in my opinion, are far more important for the university".
Bangor University said in a statement: "The increase reflects a combination of factors, including the appointment or promotion to leadership roles where salaries are benchmarked against national and standards.
"Our core mission continues, which is to provide a high standard of education and deliver research of the highest quality.
"We are committed to transparency and accountability across all our work, including salaries, the salary of the vice chancellor and Executive Board which is paid by the Remuneration Committee.
"Our leadership team concentrates on using resources responsibly to support our mission and future stability."
A spokesperson also said the vice chancellor had not received a pay rise in the current year.