New evidence showing that private-school pupils in England and Wales are not only taking easier qualifications than state-school ones, but being given the same credit for them by the most prestigious universities, will infuriate everyone who believes in fairness in education (and in life, since the routes to so many later opportunities are mapped out at school). Put together with concerns over the impact of the new GCSEs on lower-ability pupils, the sense is growing that yet another Conservative educational reform has been bungled.

The point of the changes to GCSEs pushed through by the former education secretary Michael Gove was to raise standards by making them harder. Almost all headteachers believe that this aim has been met. Increasingly, though, it appears that the price of this ratcheting up of difficulty was too high. Not only has a new schism opened up between the private and state sectors, since some private schools have refused to teach the new exams and instead opted for IGCSEs – International GCSEs – that are more similar to the old version (often retaining a mixture of exams and coursework). Existing inequalities in state schools have also been exacerbated by reforms whose overriding purpose was to make it easier to differentiate between the highest achievers (by creating two grades, 8 and 9, in place of the old A*).

How to ameliorate this situation – without causing pointless disruption, undermining public confidence or worsening the situation with regard to the recruitment and retention of teachers – is the question that the new education secretary, Gavin Williamson, must now answer. Universities must be called to account straight away for the reasoning behind their decision to treat IGCSEs as if they are equal to the new GCSEs, even though they are said by the government not to meet “the new gold standard” and are excluded from official performance tables on this basis. Given that the first new GCSEs in English and maths were taken two years ago, the onus must be on universities and Ofqual, the exam regulator, to demonstrate that the students due to begin courses shortly have had their achievements at age 16 correctly weighted. Ministers must also explain why guidance in this area has not previously been issued. At least one private-school head warned more than a year ago that state-school pupils could suffer as a consequence of being forced to sit harder exams. Why, then, did ministers leave it to Labour’s Lucy Powell to investigate?

But the problem with the new GCSEs goes beyond the knock-on effect on higher education, important though this is. For some students and teachers, the new exams were welcomed as a challenge – and those who performed well under demanding conditions deserve praise. But reports of increased stress and low morale among pupils must not be shrugged off. Putting children off learning in their mid-teens is a serious mistake. In particular, criticisms about the new exams’ unsuitability for pupils with special educational needs and in lower-ability groups must be addressed, and modifications considered.

Nor can ministers, including Mr Gove, avoid taking responsibility for the new system-wide problem that they have created – with some children of fee-paying parents now studying for different exams from their state-school peers. Given the entrenched inequalities of the British education system (though Scottish children take different exams, the private/state divide in cities such as Edinburgh follows a similar pattern), and the role of private schools in perpetuating hierarchies of social class and position, this new parting of the state/private ways was the very last thing the country needed. How can pupils, parents or the public be expected to embrace qualifications that are shunned by the most academically competitive fee-paying schools?

Mr Williamson, should he try to rectify these problems, can at least claim to be a new broom. But he – or his successor, depending on how long the government lasts – will have their work cut out. Flaws in the new GCSEs are far from the only Conservative schools policy that should, in as orderly a way as can be managed, be swept away as soon as possible.