Nigerian-born Samuel Kayode is said to have spent much of the cash on an extravagant lifestyle and buying a string of properties.
He has failed to do so, and it is feared most of the cash has been transferred to Nigeria.
The case, kept secret for almost two years, is believed to be Britain’s biggest ever education fraud.
Although Kayode was arrested in October 2012, police have yet to charge him with any crime.
Critics of academies – state schools which have control of their own finances – say the massive loss of cash calls that entire system into question.
Questions were also asked about whether Mr Gove – who lost his job as Education Secretary last week – took close enough interest in the case.
It is named after 17th century silk merchant Robert Aske who left much of his wealth to create an educational charity fund run by the Worshipful Company of Haberdashers.
The Haberdashers’ Aske’s public schools for boys and girls in Hertfordshire were founded with his money.
Three Haberdashers’ Aske’s state secondaries in South-East London – Hatcham College, Knight’s Academy and Crayford Academy – are run by the trust as a separate charitable wing funded by Mr Aske’s endowment. They were often referred to by Mr Gove in speeches. [eap_ad_1] Kayode went to work at Hatcham in 1997 and rose to become accounts manager for the whole chain.
He was paid £57,000 a year, and told colleagues of his work as a pastor in the Christ Apostolic Church, South London, peppering his conversations with ‘praise the Lord’.
Kayode’s assets and those of his wife Grace, who died aged 53 last year, were then frozen.
It appeared that huge sums of school money had been paid into a bank account in Nigeria and a company called Samak, which is said to be run in Nigeria by Kayode’s second wife Yoni, although he denies any wedding has taken place.
The trust launched a High Court case to reclaim the missing cash but the accountant denied wrongdoing and claimed ‘all transactions had been authorised by the finance director’.
He remains at large and is not facing any charges, although he is due to speak to detectives again this week.
A Metropolitan Police spokesman would say only that a man from Lambeth was on police bail.
Adrian Percival, chief executive of Haberdashers’ Aske’s Federation Trust, said: ‘The civil case found in favour of the federation and we are trying to recover the money that has been taken from us. We are obviously shocked and saddened.’
But furious parents say Haberdashers’ Aske’s has tried to hush the scandal up.
Jill Rutter, who has several children at the Hatcham academy, said in an online blog: ‘The fraud strikes at the heart of the educational establishment and shows that the current system and the freedom afforded to academies is not working. Ultimately it is our children that suffer.’
He said: ‘Sam Kayode completely had me taken, like everybody else. Nobody from the police or school has spoken to me.’