The guide, Tackling Fraud in the Charity Sector, was published this month but summarises the key points made at a joint conference of the same name held by the commission and the FAP in October.
The 20-page guide contains tips for charities on how to prevent, detect and respond to fraud, and outlines some of the most common scams inflicted on charitable organisations.
"Building a fraud-resilient charity is a job for everyone, everywhere and at every level," it says.
It warns that fraud can occur at any point between the money being given by donors to the services being received by beneficiaries, and that charities are particularly vulnerable to diversion frauds, where money is skimmed off so that not all of the donation makes it into the charity’s coffers.
Charities might also fall foul of false invoicing or employees demanding back-handers in return for grants, it says.
The guide says: "Because some fraud will inevitability leak into any organisation, you need to understand how much loss your charity is willing to accept (this is your fraud tolerance) and then put in place the systems and processes to manage that level of risk and keep exposure within acceptable limits."
It advises charities on how to ensure they have good governance and fraud risk management by creating an ethical culture, putting the right policies and procedures in place and conducting annual fraud risk reviews.
Charities are also warned to be aware of the risk of staff or volunteer fraud, online fraud and bribery and corruption, particularly in other countries.
If charities become aware of what might be fraud, it says, they should "waste as little time as possible" in taking action.
"The Charity Commission expects trustees to report fraud to Action Fraud (the UK’s national fraud and cybercrime reporting centre) and then to pursue recovery of the losses where appropriate," the guide says.