The regulator said fraudsters were contacting parents, outlining details and payment instructions for the latest school fees. Initial contact appears to be made primarily via email and often from the school's compromised email system.
The National Fraud Investigation Bureau has also seen instances where the email address used is similar to – but not the same – as that of a school. For example, it might use "nn" in place of an "m".
Victims make the required payment into a bank account in the control of the fraudsters. By the time the fraud is identified, the funds have already disappeared, the Commission said.
In several instances, there has been a strong element of manipulation to the scam, with criminals building trust with victims through contact by phone, email or other direct messaging. The fraudulent email often promises a discount for early fee payments.
The Commission is advising schools to ensure all administration staff are aware of the fraud, and parents are advised to be vigilant and always to scrutinise requests to amend payment procedures.
'Diverting precious funds'
Michelle Russell, director of investigations, monitoring and enforcement at the Charity Commission, said: "We are urging all charitable schools and parents to be alert to this. If they suspect they've fallen victim to payment diversion fraud, they should report this immediately to Action Fraud, and to the Commission, under its serious incident reporting regime.
"By working together, we will ensure these fraudsters do not prey on charities, parents and pupils in this way.
"Such scams not only divert precious funds away from the pupils and schools that need them but harm public trust and confidence in the charity and education sectors more widely."
Julie Robinson, general secretary of the Independent Schools Council, added: "We are supporting the Charity Commission in raising awareness among schools and parents, and we urge institutions to alert their stakeholders to this unlawful activity."