The charity raises about £3m a year in legacies, about 80 per cent of which is generated through the programme, which asks people to make donations in exchange for will-writing services.
The commission received a complaint about the practice in May 2008.
Its guidance document, Paying for Wills with Charity Funds, says: "We strongly advise that charity employees should never become involved in drafting an individual's will." It says the practice "is likely to be viewed with suspicion and could well increase the risk of a legal challenge to a legacy left to the charity in the will".
The charity confirmed that staff were involved in drafting wills. But a spokeswoman for the commission confirmed that it had met representatives from the charity and decided that the benefits to the charity outweighed the potential disadvantages of the scheme.
Harvey Bratt, legacy director at JNF, said that since the dispute that caused the complaint it had introduced new safeguards such as ensuring the wills drafted by the charity's staff were explained to donors by external solicitors, who would certify that the donors approved the content of the wills.