Prevent, which was introduced after the 2005 London bombings to identify and work with those at risk of radicalisation, uses a range of measures to challenge extremism.
Since July 2015, "specified authorities" such as schools, colleges, prisons and NHS Trusts have been required to have "due regard to the need to prevent people from being drawn into terrorism".
A study by three universities - Coventry, Durham, and Huddersfield, found evidence that the Prevent duty may be making Muslim students feel "singled out" and damaging their willingness to share genuine concerns about extremism.
There were also "significant concerns" about the stigmatisation of Muslim students as well as fears that the Prevent duty is making it more difficult to foster an inclusive environment for students from different backgrounds.
The research also highlighted a degree of "discomfort" and "uncertainty" among school and college staff about what some saw as the Prevent duty's ill-conceived focus on "British values".
Meanwhile, a minority of education professionals even argued that the duty might be counterproductive in preventing those who are vulnerable from being drawn into terrorism, owing to the perceived scrutiny of Muslim students stoking feelings of being marginalised by state and society.
Dr Joel Busher, from Coventry University's Centre for Trust, Peace and Social Relations, said that Prevent, as a safeguarding measure, is largely accepted by schools and colleges and has helped to foster fairly widespread confidence about the duty.
"However, linking the duty to the promotion of ‘fundamental British values' - and in particular the pressure on schools and colleges to emphasise the ‘Britishness' of these values - is often seen as more problematic," he added.
"We heard about fears that this element is both hampering effective curriculum work around shared values and democratic citizenship, and creating uncertainty about the focus of the Prevent duty."
"Widespread and sometimes acute concerns about possible feelings of stigmatisation among Muslim students highlight an urgent need for systematic evaluation of how, if at all, the Prevent duty has impacted on student experiences.
"It is likely to be some years before we are able to truly assess the impact of the Prevent duty and further research is needed."
Labour's general election manifesto, contained a pledge to review Prevent, specifically its potential to alienate communities.