The claims were made at the University and College Union Scotland's annual congress in Dundee last week, where delegates unanimously passed a motion that criticised the power of governing councils and claimed that "senior management influence is too great".
The congress heard that staff relations had broken down over redundancies, restructuring and other disputes at Strathclyde, Stirling, Glasgow, Glasgow Caledonian and Robert Gordon universities.
A second motion, also passed unanimously, called on UCU Scotland to organise members to provide effective opposition to job cuts and "degrading working conditions".
Addressing delegates, Claire Baker, education spokeswoman for Scottish Labour, agreed that changes should be made to university governance, stating that higher education institutions "are not being run and are not accountable in the way that they should be".
The Scottish National Party's green paper on higher education "raised a lot of questions but didn't really come up with any answers".
"We need a consensus as to how we reform (university governance), but we agree that there needs to be change in how we make decisions in universities," Ms Baker said.
Other speakers claimed that university heads were using financial constraints as an excuse to cut jobs and get rid of individuals they disliked.
Lesley McIntosh, president of UCU Scotland, said: "The attacks have come from all corners and have been constant."
Ralph Catts, president of the Stirling branch, described Scottish university management as a "farce". "Cronyism is the order of the day at several universities in relation to the university court...they have no independent information and they are basically friends of friends. The consequence is that there is not genuine accountability for senior management," he said.
Bill Johnston, vice-president of the UCU branch at Strathclyde, said that it was "no longer sufficient to firefight institution by institution". Instead, he argued, "we need to raise the consciousness that Scottish higher education is effectively in crisis".
But Gordon Watson, president-elect of UCU Scotland, was positive. He said it was "amazing" that for every pound spent on higher education in Scotland two pounds were generated, with up to five pounds generated in major cities.
"There is no reason for any of the cuts," he said. "The future for us is actually rosy.
"If this country is going to go forward (participation in higher education is) going to have to be higher (than 50 per cent), so any cuts in the next year or two will be temporary.
"Higher education is the way countries will pull themselves out of the problems they've got."