Based on data from the Universities and Colleges Admissions Service, the commission found women are now a third more likely to enter higher education than men after the overall gender gap in admissions grew compared with 2010.
Among UK residents, 134,097 women aged 19 and under were accepted to English universities in 2012 compared with 110,630 young men.
That was a 2.6 per cent decline since 2010 for girls and 4 per cent for boys, while there was a 5.9 per cent decline for girls and a 7.5 per cent decline for boys since 2011 when enrolments peaked just before the introduction of higher tuition fees.
In the 40 per cent of English neighbourhoods where university participation is lowest, there were 1,700 fewer boys aged 19 and under who were accepted for places in 2012 than in 2011 – a decline of 5.4 per cent compared with the 3.7 per cent fall for young women from the same areas.
When compared with 2010, the number of young working-class male acceptances fell by 1.4 per cent, while young female acceptances increased by 0.9 per cent, the study says.
“Today’s report shows that the first year of fees produced a worrying widening in the university gender gap,” said the commission’s chair Will Hutton, the former editor-in-chief of The Observer, now principal of Hertford College, Oxford.
“In working-class areas, there has been a decline over two years in the number of boys accepted for university, while the number of girls accepted has risen,” he said.
“This is particularly worrying, because women are already a third more likely to go to university than men, and the danger is that the higher fees may be having a disproportionate impact on men, who are already under-represented at university.
“The government, universities and schools should consider whether specific measures are necessary to address their concerns.”
The report follows concerns expressed by universities and science minister David Willetts in January over a growing gender gap, raising the possibility that white, working-class boys might be treated as a target area for universities in the same way as students from ethnic minorities.
Sally Hunt, general secretary of the University and College Union said: “This government has made it much harder for people to consider university and it is worrying that the number of boys from the poorest backgrounds going to university has fallen.”
Total acceptances to UK universities fell from 431,000 in 2011 to 407,391 in 2012 - a drop of 23,844 or 5.5 per cent, making UK acceptances the lowest since 2008, the reports says.
The commission, which also includes Sutton Trust chairman Sir Peter Lampl and broadcaster Libby Purves, also found fewer students from poorer neighbourhoods were reaching the UK’s most elite universities.
Acceptances to the top 13 universities based on league table rankings – Birmingham, Bristol, Cambridge, Durham, Edinburgh, Imperial College, LSE, Nottingham, Oxford, St Andrews, UCL, Warwick and York – fell by 0.1 per cent for applicants from England’s lowest participation neighbourhoods, but rose by 4.7 per cent for those from the most advantaged areas.
Students from the richest fifth of neighbourhoods are ten times more likely than those from the poorest fifth of neighbourhoods to go to one of the top 13 universities, the study finds.
A spokeswoman from the Department for Business, Innovation and Skills said more recent application figures for 2013 show that the proportion of 18 year olds from the most disadvantaged backgrounds is the highest on record.
“However, significant challenges remain, and there continues to be a large gap in higher education participation between men and women,” she said.
“That is why we have brought in annual access agreements, launched a Student Finance Tour and increased student support through higher maintenance grants and a new National Scholarship Programme.”