The investigation - funded by the Scottish Government - also reveals that a significant proportion of Jews are considering leaving the country due to anti-semitism.
Four out of five of those surveyed felt that events in Israel and Palestine in 2014 had negatively affected their life as Jews.
And one in five expressed concern with Scottish councils raising the Palestinian flag in solidarity with the state.
The Scottish Council of Jewish communities, which conducted the study, called the results “extremely sobering”.
They wrote that their survey “was entirely dominated by expressions of insecurity and alienation. “
“Most tellingly, the person who said in 2012 that Scotland is a ‘darn good place to be a Jew’ told us less than two years later that ‘I feel alienated, and no longer Scottish first, then Jewish.”
The report contains various further accounts of anti-semitism experienced by respondents and their families.
One woman stated that she could not discuss being Jewish “without being attacked in some shape or form”.
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Another respondent said that his son was “bullied by some boys for being Jewish” when he attended secondary school.
Gabriel Phillips, a Jewish student living in Edinburgh, said that he believed many attempted to justify anti-Semitism under the guise of supporting Palestine in the Israel-Palestine conflict.
He said: “You have a number of people and institutions in Scotland that attempt to legitimise anti-semitism under the guise of being ‘pro-Palestinian’.
“An example I often use is that while I was at a party in Edinburgh. I met somebody who upon discovering I was Jewish went ‘You’re Jewish? F*** Israel’. These sorts of things are becoming all too common, which means that they are much more likely to keep quiet about their background.”
Mick Napier, of the Scottish Palestine Solidarity Campaign, said: “Anti-semitism, as a species of racism, is disgusting and needs to be opposed, but it is difficult to take seriously anyone who threatens to emigrate from Scotland due to a Palestinian flag being flown by Scottish city councils.
“It may be that some Anti-semites use Palestine as a cloak for their bigotry but virtually all those active in support of the Palestinian people, and all who are active in our campaign, are motivated by anger at the crimes of the State of Israel.”