The UCU Scotland union, which represents lecturers, said institutions such as Glasgow and Edinburgh were increasingly using the controversial contracts to employ staff.
Zero-hours contracts – sometimes known as "hours to be notified" – tell staff how many hours they may be required to work, but the employer has no obligation to provide that employment.
The benefit to the university is they can pay individuals as and when required, but critics argue their use leads to a chronic lack of job security that in turn may lead to lecturers being unfocused.
Traditionally used in low-paid jobs, zero-hours contracts are now increasingly being used by employers such as the NHS.
A recent survey at Edinburgh University found 27% of staff are on such contracts, rising to 47% for those in the College of Humanities and Social Science.
Mary Senior, Scottish official of the UCU, said: "The statistics from Edinburgh go some way to revealing the true extent of the casualised workforce in Scottish higher education. It is deeply concerning that over one-quarter of staff at one of Scotland's leading institutions are on zero-hours contracts, with no job security and inferior terms and conditions.
"This casual nature of employment is inefficient, unfair and can be detrimental to the student experience. It also comes at a high personal cost to those staff on zero hours contracts, bringing financial insecurity to individuals and their families, and denying staff any real opportunities for career development."
Ms Senior said Edinburgh was not alone in using casual contracts, with a "proliferation" of them at Glasgow University and other institutions.
"Employers tell us the work or volume of students for courses is unpredictable, and this is why they use casual workers," she added. "However, we are in a period of funding stability and our members can point to work patterns, which makes us question this rationale."
Robin Parker, president of NUS Scotland, which represents students, attacked the practice. "Many of these casual employees are postgraduate students who will have to somehow juggle multiple jobs because they have no way of knowing when their next paycheck will come. These kinds of contracts also affect undergraduate students, because staff with little job security are likely to face greater stress, and this could affect teaching quality."
However, a spokesman for Edinburgh University said "hours to be notified" staff all benefited from the same terms and conditions as full-time staff. "We employ staff on 'hours to be notified' contracts in order to provide flexibility in the way that we provide services to students," he said.
"Many of the staff working under these contracts are students at the university who benefit from earning extra money during their time here while gaining valuable work experience."
A spokesman for the University of Glasgow said: "We take employment responsibilities very seriously. A zero-hours contract with no specified hours of work is appropriate in situations in which the requirement for work to be undertaken is planned and agreed over a period of months or longer, but the pattern of work is irregular and can vary from week to week or month to month."
A spokeswoman from Universities Scotland, which represents university principals, questioned the Edinburgh data, saying: "It appears to have been gathered from a voluntary and self-selecting survey of staff. If so, this is not a rigorous means to present an evidence base."