Shawcross, who headed the Charity Commission for England and Wales between 2012 and 2018, led the watchdog in a period in which it was strongly accused of bias by rights groups.
A Guardian analysis in 2014 revealed that more than a quarter of statutory investigations launched by the body since April 2012 had targeted Muslim organisations.
Remarks made by Shawcross about Islam have also resurfaced.
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While serving as a director of the neo-conservative Henry Jackson Society think tank in 2012, Shawcross appeared to indicate belief in a clash of civilisations of sorts between Europe and its Muslim citizens.
"Europe and Islam is one of the greatest, most terrifying problems of our future. I think all European countries have vastly, very quickly growing Islamic populations," Shawcross said in a video filmed at the time.
Critics have also pointed out remarks made by Shawcross in his 2012 book 'Justice and the Enemy', in which he appears to defend the United States' use of torture at Guantanamo Bay.
In the book, Shawcross describes waterboarding as an "enhanced interrogation technique", adding that the gruelling torture technique is "very likely" to produce valuable information for interrogators.
Britain's largest network of Muslim organisations slammed Shawcross' appointment in a statement on Thursday.
"William Shawcross is singularly unfit to be a neutral and fair assessor of this government policy, which has been criticised for unfairly targeting British Muslims, given his frightening views about Islam and Muslims," the Muslim Council of Britain said in a statement.
"It is ironic that a policy supposedly charged with preventing extremism is to be scrutinised by a person who holds hostile views on Islam and Muslims, who has links to people with extreme views on us, and who defends the worst excesses of the so-called ‘War on Terror’," the statement added, describing the appointment as "Trumpian".
Shawcross' appointment earlier this week followed 13 months of delay by the UK government, after first announcing a review of the Prevent Strategy in January 2019.
Civil liberties and rights groups, including Amnesty International, have long called for an independent review of the anti-radicalisation strategy. Activists and Muslim bodies say that Prevent has created an environment of fear and discrimination against Muslims.
Under the strategy, schools, NHS trusts, local authorities and prisons have a statutory duty to report concerns about individuals perceived to be at risk of radicalisation.
Recent figures show that that just 11 percent of Prevent referrals were deemed to be legitimate radicalisation risks.
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