A report on Rugby School, whose old boys include archbishops Archibald Tait, Frederick Temple and William Temple, said: "The prospectus claim that formal religious education plays a vital part in engendering moral values is open to question."
The Independent Schools Inspectorate said: "There is no established religious studies department to provide the intellectual and academic foundation to support one of the school's professed aims."
But overall the inspectors praised the "remarkable" school, which costs pound;17,550 a year and boasts the motto Orando Laborando, "By prayer and work".
They said it had "a warm, busy, productive atmosphere" as well as good standards of achievement. All of last year's Year 11 girls gained five or more A*-Cs at GCSE, as did 97.8 per cent of the boys.
The report applauded pupils' attitudes to learning and the quality of teaching and resources, including use of ICT.
And it noted that the bullying which featured large in Tom Brown's School Days, based on the school, was no longer a problem, saying: "A suitable school anti-bullying policy is reinforced in a number of departmental handbooks. Bullying incidents are relatively rare and when they do occur the school responds effectively."
However, it said the school had not produced an overall development plan and that planning and documentation needed to be addressed.
Headteacher Patrick Derham said: "The chapel is right at the heart of the school." He said divinity was taught in the lower school but not examined, and that Rugby was considering introducing an RE GCSE.