Extremist books were found in prison libraries seven months after the Government was told they should be removed, according to reports.
The presence of Islamist literature, some encouraging jihad, in prisons was reported to the Ministry of Justice in November, according to the BBC.
But the texts remained in prison chaplaincies until June 2016.
The Ministry of Justice said a thorough assessment of the books had to be carried out before they could be removed.
The books include The Way Of Jihad by Hassan Al-Banna and Milestones by Sayyid Qutb, the BBC reported.
Both books have been linked to the the radicalisation of young Muslims.
Former prison governor Ian Acheson led a review into radicalisation in jails that found the books.
At the beginning of July he reported to MPs that Islamist extremism was a growing and potentially lethal problem in prisons and there were numerous examples of literature of an extremist nature in chaplaincies, while the recruitment, training and supervision of prison imams was "seriously deficient".
Writing in the The Times he said: "Young men in our prisons are at risk of being indoctrinated by a warped ideology that mobilises their capacity for violence and, that at the most extreme, provides them with theological permission to kill the unbeliever.
"Noms (the National Offender Management Service) must do more to prevent its inmates from becoming seduced by an Islamist world view and potentially taking a weaponised version into the community."
A Ministry of Justice spokeswoman said: "We take the threat of radicalisation and extremism extremely seriously and will not tolerate extremist literature in our prisons.
"That is why we carried out a thorough and objective assessment of these texts and then removed them from all establishments.
"The new Justice Secretary will now work closely with the Home Office and other agencies to tackle the important issue of Islamist extremism in prisons."