The survey questioned 553 Catholics in seven of Scotland's eight dioceses as part of the Lanarkshire-based Conforti Institute's Anti-Sectarianism project, which is funded by the Government.
A report on the findings said many respondents, particularly those in Glasgow and Motherwell, believed Orange Walks to be "an expression of hatred against the Catholic community".
They described feeling "fear and a sense of unease, being intimidated, threatened and offended when they think about them".
They also believed there were an excessive number of Orange Walks and that the events should be restricted to public parks.
The report said there was a reluctance among many respondents to speak out about sectarianism because "they fear that even raising the issue invites the response that sectarianism in Scotland will be solved in Scotland with the closure of Catholic schools".
The Act of Settlement, which bars Catholics from acceding to the throne, meant "Catholics are treated constitutionally as second class citizens", said the report.
It added: "The Scottish Government is fudging the issue: it is really about institutionalised sectarianism."
Researchers said social media was also cited among younger participants as the main venues for intolerance on both sides because there was "a feeling that more extreme things can be expressed".
Report author Dr Geraldine Hill said sectarianism meant different things to different people.
She added: "The perception of sectarianism primarily being about anti-Catholicism in Scotland is a topic of debate. Some would take that view, others believe that things have moved on considerably or believe that both an anti-Christian and secular agenda is more important."
Historian Tom Devine said opinion polls regularly skewed the debate on sectarianism, with far fewer respondents able to report any direct experience of violence or discrimination compared to the number who perceived sectarianism to be a problem.
He said the Orange Order had developed out of anti-Catholicism and a defence of Protestantism.
"Most Scots who are not members of that organisation regard those walks as potentially intimidating," he added.
But he questioned why public money was being spent on an "anti-sectarianism industry".
"When this phenomenon is least alive, least livid, compared to the way it was in the 1950s, 60s, and 70s, when it was a vicious force in Scottish society, why is it that when it is on its deathbed, or very close in terms of decline, is it that we have had this massive rise of an anti-sectarianism industry? Whereas when it did exist, people regarded it like a bad smell at a middle-class dinner party - everybody knew it was there but nobody was willing to talk about it."
A Scottish Government spokeswoman said the Government was committed to tackling sectarianism and was spending £9 million in three years to help eradicate it.
She added: "We welcome the Conforti Institute report which will help to build our understanding of how communities across Scotland experience sectarianism."