The commission’s alert comes after a number of cases that involved police and UK ports officers seizing charitable funds held as cash, with about £4m seized at ports by the MPS Counter Terrorism Command in the past two years.
The commission said it had received an increased number of enquiries from the police about people who claimed to be carrying money on behalf of charities.
In its alert, the commission said the risks involved in cash couriering included its use by terrorists and criminals to move money, the likelihood of the money being seized if the end use of the cash was not satisfactorily accounted for, and the substantial length of time and cost involved in retrieving seized money.
The commission said that carrying significant amounts of money made cash couriers targets for criminals, that cash couriering was difficult to audit, and that because there were no requirements for couriers to register as money service businesses with HM Revenue & Customs, there was less assurance about their quality and reliability.
The commission recommended that charities use formal banking systems instead, and use cash couriering only in exceptional circumstances when other means of transferring funds were not available.
Michelle Russell, director of investigations, monitoring and enforcement at the Charity Commission, said: "The commission has seen an increase in the number of charities having cash seized from their fundraisers, agents and representatives at the UK border. The effects of a cash seizure include the charities’ beneficiaries losing out, an impact on the charities’ activities and the loss of donor money, including the permanent loss of funds.
"The commission’s advice is simple: don’t use cash couriers unless there is no other possible means of moving money, and follow the regulatory advice issued."
Commander Dean Haydon, head of the Counter Terrorism Command at the MPS, said: "Cash couriering is a high-risk activity for any organisation or individual to undertake, and is a method known to be used by terrorists and criminals. My advice to all charities is to send money safely and not to use a cash courier.
"If you do, there is a real risk that without proper documentation and a clear explanation of the source and destination of the cash, the cash will be seized by the police and ultimately lost to the charity."