Those opposed to plans to set public sector pay regionally, rather than nationally, tend to focus on concerns about exacerbating inequality. Were state salaries in the cash-strapped North to be frozen while their Southern counterparts continued to rise, the reasoning goes, then existing geographical divisions would only be entrenched yet further. The latest study of Britain's schools, however, turns the argument on its head – and heaps fuel onto one of the more combustible of the Government's policy proposals.

According to Bristol University's research, state secondaries in wealthier areas are struggling to recruit and retain teachers because national pay agreements do not allow them to offer more generous salaries to reflect higher local living costs. More troubling still, the situation is costing their pupils as much one whole GCSE grade.

The findings will be music to the ears of the Education Secretary. Tackling the (in his view) inefficient and iniquitous national pay scale is a central part of Michael Gove's reforms. And ahead of a report from the independent teachers' remuneration board this autumn, he has made clear his support for a more flexible approach including both regional differentiation and performance-related wages.

National pay agreements have already been significantly eroded. Both "free" schools and academies – which will account for half of all state secondaries by September – are able to set teachers' salaries themselves. Thus far, though, few have taken advantage of their new-found freedom, in part out of an unwillingness to provoke the teaching unions, in part out of institutional inertia. Only by tackling national pay more directly, Mr Gove has concluded, can he change the culture and introduce some much-needed competition.

In fact, it is not just teachers' salaries on the table. The Chancellor has his sights on similar changes across the public sector. But the plan has already run into the political sand – even while formal reports from various Pay Review Bodies are still under consideration – thanks to outspoken opposition from both Liberal Democrats and Tories with Northern constituencies.

Even more reason, then, to support Mr Gove's efforts in the education sector. Although critics' concerns about regional inequalities cannot be dismissed out of hand, the case in favour of flexible public sector pay is the more compelling one. After all, national wage levels result in inequalities of their own – with public sector workers in one area enjoying a standard of living wholly unaffordable to colleagues elsewhere. They also skew regional labour markets, pushing up private sector salaries and making life harder for local businesses.

It is perhaps fitting that the Education Secretary is leading the charge. As one of the Coalition's most ambitious reformers, instituting the biggest shake-up of the state school system for decades, he has proved his appetite for controversy. But with all three teaching unions already warning darkly of industrial action, it is on regional pay Mr Gove faces his stiffest opposition yet. It can only be hoped that clear evidence that educational standards – and pupils' lives – are suffering will encourage teachers to think again.

There are unintended consequences of which to beware. Schools in the most disadvantaged areas may need to pay more, for example, in order to attract teachers best able to deal with the significant challenges they face. But the caveats do not outweight the benefits. Providing the focus is on flexibility – allowing schools to set levels as they see fit rather than setting regional levels – Mr Gove's trailblazing proposals have much to recommend them.