After a lengthy investigation, the Independent Broad-Based Anti-Corruption Commission has charged Mr Napoli, the alleged ringleader of the scam, with more than 150 criminal offences.

These include conspiring to defraud, knowingly dealing with and concealing the proceeds of crime and producing false documents.

Mr Napoli will appear before Melbourne Magistrates Court later this month alongside his cousin Carlo Squillacioti and former Keilor Heights Primary School principal Michael Giulieri.

The anti-corruption watchdog has also charged his distant cousin, Daniel Calleja, who will appear before court in March.

"IBAC's investigation focused on allegations that senior departmental officers misappropriated funds from the Department's budget, through false and inflated invoicing as well as arranging payment of inappropriate expenses such as excessive hospitality, travel and personal items," a spokeswoman said.

The news was welcomed by Education Minister James Merlino and many principals, who are keen to move on from one of the most sordid chapters in the history of Victoria's Education Department.

Mr Napoli, who was the department's finance manager, allegedly funnelled millions of dollars of funds earmarked for needy schools to companies run by his relatives between 2007 and 2014. These allegations were at the centre of IBAC's Operation Ord, which held public hearings in 2015.

The former department executive has been linked to at least $1.9 million in profits which allegedly benefited his relatives and associates, and a further $4.4 million in suspicious transactions and contracts.

A long-awaited report by IBAC released last year found that Mr Napoli obtained the funds through so-called "banker schools" by "carefully selecting and grooming principals and business managers".

These principals allegedly signed off on false invoices and received a small cut of the transaction.

"The conduct uncovered during IBAC's investigation was underpinned by a malevolent culture of non-compliance and entitlement," the report said.

It also concluded that former acting secretary Jeffrey Rosewarne – who has not been charged – spent tens of thousands of school funds on his wife's travel expenses, wine, home office furniture and his 50th birthday party.

An expensive hairpiece worn by Mr Napoli also made headlines during the 2015 hearings and gave "bigwig" a new meaning. Secret recordings allegedly revealed that the senior official wanted to use taxpayer funds for his expensive toupee.

Mr Giulieri allegedly conceded during the 2015 hearing that he acted corruptly when he wrote a fake letter requesting $30,000 to pay for work that was never completed.

The former principal allegedly wrote a bogus application requesting Education Department funds to pay Mr Napoli's son for work he never did.

The saga has been a major embarrassment for the Education Department, which has abolished the banker school system which was allegedly abused by the officials.

A Department spokesman said that the senior executives embroiled in the corruption no longer worked with the Department.

"The Department has actively pursued a comprehensive reform agenda in the wake of these investigations, putting integrity at the heart of everything we do. This includes changes to procurement and auditing practices and financial training for schools as well as reviewing policies around travel, gifts and hospitality and the launch of a new, confidential 'Speak Up' service."

Mr Merlino said that the behaviour exposed during the hearings was "nothing short of disgraceful".

"Victorian families have every right to be outraged at this behaviour. The public expects and deserves better from its public servants," he said.

Australian Principals Federation president Julie Podbury said that she looked forward to the matter being resolved.

"Every education dollar is so hard won. You hate to see a dollar wasted in any way," APF president Julie Podbury said.

"We would be pleased to see the matter properly dealt with."

Many of the officials implicated in Operation Ord were also involved in the disastrous $180 million Ultranet IT project, which is at the centre of a separate IBAC investigation called Operation Dunham.