Female graduates earn little more than many men of the same age without degrees, according to official data that shows even superior qualifications are not enough to catapult women across the pay gap.

The graduate pay figures, collected from tax data by the Department for Education and analysed by the Institute for Fiscal Studies, cast a new light on who gains most from attending university in England, at a time of debate about higher education’s value for money.

The new study is the first to compare the rewards of a university education with the earnings of non-graduate workers of the same age and with similar school-level attainment.

According to the IFS’s analysis, male graduates receive an income boost of 6% compared with what they might have earned had they gone straight into the workforce after school.

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For women the impact was far larger: female graduates were found to earn nearly 50% more than non-university educated women. But that only brought them up to similar income levels of male non-graduates, with each earning about £30,000 on average by the age of 29.

The IFS’s Jack Britton said that in terms of employment, women had the most to gain from a degree because those without a degree received far less pay than men without one.

“For women, going to university is a very good investment, for men it’s less clear – there are a large class of men doing courses that have zero or negative monetary value, so it’s a question for them of if it’s worth doing,” Britton said.

The figures confirm the huge variations in earnings between graduates of different subjects and institutions. While medicine and economics offer the biggest potential pay boost, graduates in subjects such as creative arts and English have lower incomes than they would if they had avoided university.

Sam Gyimah, the higher education minister, used the figures to celebrate the benefits of universities in England while telling some institutions that they risked regulation by the Office for Students.

While 85% of students got a “significant, positive return” from higher education, Gyimah said, “it is also clear from the analysis that there are a clutch of courses at certain universities which are not delivering the financial outcomes for students”. He said the Office for Students would be “cracking down on courses that don’t offer value”.

Asked if it was realistic to punish universities today for the careers of students who graduated a decade earlier, Gyimah said: “Yes, the data is from 10 years ago, but I have been careful to highlight that it is one of a number of indicators that we look at, it’s not the only indicator.

“I think it is pretty serious if there is a course that 10 years ago did not deliver value, and that course is still being put on for future and prospective graduates to take. I think the intervention should be swift in that case.”

The IFS analysts noted that people who went to university usually had better school-level exam results and came from richer families, and so would be expected to have more lucrative careers and higher earnings in any case.

The figures are derived from longitudinal observations following people who took GCSE exams between 2002-07 up to the age of 29. The study included graduates from 140 higher education institutions in 30 subject areas.

Although women receive a much larger uplift in their earnings after completing a university degree, the statistic is flattered by the much lower pay that non-graduate women receive.

The IFS data shows that by 29, female graduates were earning just over £30,000 on average – roughly the same as the nearly £30,000 a year paid to men with good GCSE results who did not go to university, but around 50% more than non-graduate women, on £20,800 a year.

Male graduates were earning on average £37,000 by the age of 29.

In recent years some commentators have been alarmed by the gap between men and women taking undergraduate degrees in the UK, with the participation rate of women now 10 percentage points higher than that of men by the age of 19.

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The IFS noted that one in three male graduates (33%) attended universities that failed to improve their incomes above those of non-graduates, while only one in 100 female graduates did the same.

The authors said differences in earnings could be the result of “unobservable traits” such as soft skills, while incomes could also be affected by market demand. Hours worked, students loans and the non-monetary benefits of higher education were also not taken into account.

Nicola Dandridge, the chief executive of the Office for Students, said better financial prospects were only one reason why people in England went to university. “But universities should scrutinise this data carefully, and some will need to ask themselves tough questions about how well they are preparing students for life after graduation,” she said.