Research by the University and College Union Scotland found 66% of universities had staff on the contracts, with slightly less than half of those polled admitting they had more than 100 staff on the deals.
These include Glasgow, Stirling, Edinburgh Napier, West of Scotland and Abertay in Dundee.
At the remaining institutions that took part in the study, the number of people employed on zero-hour contracts ranged from eight to 44, although Edinburgh University had more than 2000 people on them.
The contracts inform staff how many hours they may be required to work, but the employer has no obligation to provide that employment. They are also known as "hours to be notified". It means an employer can pay the staff who sign them as and when required and they can also benefit employees who want flexibility over their own working patterns.
Typically, universities employ visiting tutors and researchers, who are only working for a short time, on these contracts, rather than their own full-time staff.
However, critics argue their use leads to a chronic lack of job security and believe they are spreading from low-paid jobs to the public sector and employers such as the NHS.
Research released last month suggested there could be about one million workers in the UK on zero-hours contracts - a marked increase on revised estimations from the Office Of National Statistics of just 250,000.
The University and College Union Scotland said the survey findings "shone an important light on the murky world of casualisation" among teaching staff.
President Dave Anderson said: "As well as the uncertainty that comes with being on a zero-hours contract, many staff suffer exploitation through other temporary contracts. Their widespread use is the unacceptable underbelly of our universities.
"Employers cannot hide behind the excuse of flexibility. The flexibility is not a two-way street and, for far too many people, it is simply a case of exploitation.
"We are encouraged the Government and the Opposition have said they will be looking at zero-hour contracts, but neither has yet said anything that will give the thousands of people subjected to these conditions much hope."
A spokesman for the University and Colleges Employers Association said the focus on head count was not a good measure because of a high number of staff doing very small numbers of hours.
He said: "The association is well aware of the trade unions' interest in understanding the types of flexible employment used by the sector to meet the changing demands on higher education institutions.
"It has offered joint work to develop a better understanding of practice and trends in relation to all types of flexible employment in higher education, acknowledging the unions' particular concerns about zero-hours contracts.
"Our members have stressed they use casual contracts in circumstances where the demand for work of a particular kind is variable or unpredictable, such as visiting specialist lecturers, or student employment of various kinds, such as ambassadorial roles or assisting in special events."
The Educational Institute of Scotland teaching union, which is conducting its own survey, said higher education employers should explain why the figures were so high.