Among the prohibited titles are a tract described as the'Mein Kampf'of Islamist terrorism, a pamphlet extolling the virtues of violent jihad and a book urging Muslims to fight and subjugate unbelievers.
According to a BBC report, an inspection team led by Ian Acheson, a former UK Home Office official and former prison governor, first alerted the UK's Ministry of Justice (MoJ) to the presence of the books in November 2015.
Acheson then submitted his report in March 2016 and the order to remove the books was only made on or after June 20.
In evidence to the House of Commons Justice Committee last week, he said his investigation had found "numerous examples" of books that were "extremist in nature in prison chaplaincies".
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The banned titles include 'The Way of Jihad' by Hassan Al-Banna; 'Milestones' by Sayyid Qutb; 'The Lawful and Prohibited in Islam' by Sheikh Yusuf al-Qaradawi; 'Towards Understanding Islam' by Syed Abul Ala Maududi; and 'Fundamentals of Tauheed' by Bilal Philips.
Among them were high-security Category A prisons in England and Wales.
Prisons in England and Wales held 12,328 Muslim inmates at the start of this year, 131 of them convicted terrorists. A further 1,000 were considered to be at risk of radicalisation.
"We take the threat of radicalisation and extremism extremely seriously," a Home Office statement said.