The Office of the Schools Adjudicator (OSA) has published a report claiming the London Oratory has an unfair admissions policy and could be breaking the law.
Its investigation was prompted after a complaint from the British Humanist Association last April.
It says the school in West London discriminated against non Catholics by 'not allowing for the admission of children of no faith' and having an admissions policy that made it harder for students from a certain social background to get a place.
London Oratory is also accused of giving applicants priority on the basis of expecting practical or financial help from a child's parents.
Former students at the school include the sons of ex Prime Minister Tony Blair, Lib Dem leader Nick Clegg, and deputy leader of the Labour party Harriet Harman.
The OSA found 105 aspects of the school admissions code were broken over a two year period.
Its report also found the school not only has a lower proportion of pupils from non-white backgrounds compared to the local community but also to all Catholic state secondaries in the capital.
Adjudicator Dr Bryan Slater said: "I do not believe that the school can claim that its ethnic composition is even representative of that of the Catholic children attending schools in the part of London in which it is located.
"It seems to me instead that the diversity within the school is the lowest, or very nearly the lowest, of that found in all 13 schools.
"From the evidence which I have seen there is good reason to believe that the admission arrangements which the school uses have the effect of acting to produce at the very least a degree of social selection."
The OSA will now order the London Oratory School to change its admissions policy to ensure a fairer entry assessment.
The boys comprehensive says on its website it aims to "assist Catholic parents in fulfilling their obligation to educate their children in accordance with the principles and teachings of the Church."
The headmaster, David McFadden, told The Telegraph newspaper: "The Office of the Schools Adjudicator has made four determinations against this School in the past six years, the most recent of which was again challenged successfully.
"Today the Adjudicator's Office has now, it seems, suddenly found a further 105 aspects of our admission arrangements which apparently breach the School Admission Code. The School Governors once again reserve the right to refer this determination to Judicial Review."
The Department of Education said: "All schools must abide by an adjudicator's determination. We expect them to amend their arrangements to comply at the earliest opportunity."