Ofsted, the school's inspectorate, claims St Benedict's Catholic School in Bury St Edmonds is not preparing people for life in Britain and is leaving pupils vulnerable to extremism.
It's in the wake of new rules following the Trojan Horse plot that means schools must ensure young people are not open to radicalisation.
The CES is now calling for an apology and explanation from Ofsted. Paul Barber, director, told The Telegraph: "We are extremely concerned that Ofsted is publicly listing St Benedict's as one of the 11 schools which 'were not preparing pupils for life in Britain today'.
"These concerns cannot be found in the School's Ofsted report. These concerns cannot be found in the School's Ofsted report.
"This is an unjust and unsubstantiated accusation and we hope Ofsted will clarify this matter and apologise to the school and parents for the confusion and upset caused.
"We welcome the role of Ofsted in ensuring accountability, transparency and inclusive education for all, regardless of belief.
"However it is essential that Ofsted provides support and clarification for their own staff on the matter of British Values to prevent mistakes like this from recurring."
An Ofsted spokeswoman said: "Inspectors found that a number of the schools could have been doing more to prepare pupils for life in Britain today.
"This definition covers a wider range of issues other than dealing effectively with extremism and radicalisation, and includes how a school's curriculum and other activities raise the pupils' awareness of different aspects of how our society works.
"Sir Michael Wilshaw is looking forward to meeting representatives from the Catholic Education Service this week as part of his commitment to meet education leaders from the different faith communities to discuss Ofsted's inspection frameworks and guidance."
Paul Barber, director, Catholic Education Service: