The warnings come in the commission's new Charities and Publishing Companies report, which is based on an examination of publishing companies that fundraise on behalf of specific charities. It outlines how publishers approach small businesses asking them to support named charities by buying ad space in diaries, calendars, and other printed material.
The investigation found that prices of up to £700 are being charged to companies for ad space, yet charities receive returns as low as 6 per cent.
The report is based on a 10-month study of 10 charities, including Cancer Journey, Kids in Action and the Association of Wheelchair Children.
It also uncovered aggressive selling tactics and warns that these can bring the charity's name into disrepute.
"A charity's name and reputation are precious assets which trustees must protect by ensuring they are not associated with underhand practices," said Simon Gillespie, director of operations at the Charity Commission.
"The report sets out some best practice guidelines which we would encourage charities to follow. Working with reputable publishing companies can be an effective way for charities to raise funds, but as with any commercial partnership, thorough homework is a must," added Gillespie.
Six of the charities have terminated their agreements with their commercial partners following advice from the commission, while the other four have had help to improve their deals.
The report, published on the commission's website, suggests that charities listen in to phone calls made by telesales staff to ensure they follow certain rules, such as making a solicitation statement which outlines how much of the prospective buyer's payment will go to charity.
The commission hopes to create awareness of the report by sending it to charity press and small business magazines to influence both affected parties.