The Government's London Challenge proposals for the capital are expected to be unveiled later this month. These include plans for more city academies and improving teacher retention and recruitment. But there will be little new cash to tackle underachievement.
The strategy aims to transform secondary education in the city and the input of Professor Brighouse, - the charismatic and widely repected former Birmingham schools chief - is seen as crucial to making it work.
But sources close to the commissioner say his enthusiasm is wavering because of concerns that he will not get the funding he needs.
"Without bespoke new money I doubt whether even his enthusiasm is going to overcome the difficulties created by the funding crisis, which is at its most marked in London," said one.
"Headteachers whose schools he has visited have seen how concerned he is about the situation."
The news comes only days after Professor Brighouse described the funding crisis as the "worst of times" to the National Association of Head Teachers' conference in York.
"It is the worst dislocation of funding we have all experienced in our working lifetime," he told delegates However, Professor Brighouse also paid tribute to the efforts of education minister Stephen Twigg, who is working with him on the London Challenge, to solve the problem.
The London Challenge strategy is seen by Downing Street as a model for public-sector reform.
Ministers hope that it will achieve the twin goals of tackling disadvantage and persuading middleclass parents that inner-city state schools are good enough for their children.
It is expected to encourage councils to use existing money, such as the leadership incentive grant, to tackle underachievement. It is also likely to put greater emphasis on teachers' continuing professional development.
Around 20 new secondary schools are planned: some city academies, which rely on central funds and private sponsors; some paid for through the Private Finance Initiative; and some funded by "traditional methods". Some existing secondaries would also be reopened as city academies.
Mr Twigg denied reports that a "hit-list" of 50 poorly-performing London schools had been drawn up, but said that some had been identified as needing more support.