The move came after an anonymous warning about the company's selling methods was posted on an Institute of Fundraising internet forum and one of the charities contacted Third Sector.
Health Care Communications, which sells advertising spots on the intranet phone directories it supplies free to health trusts, says it has suspended marketing to the sector and is conducting an investigation into 16 cases.
Mike Cunningham, managing director of HCC, said: "I am grateful this has been brought to our attention and have taken steps to rectify the situation. All relevant charities have been contacted to clarify their marketing and sponsorship arrangements with us."
One of the charities was Afghanaid, which was told by HCC it was seeking proposals from small international charities for a fundraising partnership with a health trust employing 28,000 staff.
"The carrot was that the partnership would involve an email to the staff from the chief executive of the trust and opportunities for fundraising and payroll giving," said Adele Bird, head of fundraising at Afghanaid.
"It was not the sort of thing I wanted to ignore.
"They made out they could turn it into something big. But I discovered the reality was that we would pay £6,000 for the ad button, we would get a 25-word mention in an email and on a poster in staffrooms, and the rest would be up to us."
When Bird saw the warning about the company on the institute's trusts and statutory special interest group e-forum, she contacted the health trust. She was told the charity's advert would be like any other and no partnership was envisaged.
She then told HCC she was withdrawing from the deal. "I feel absolutely livid about the whole thing, not least because I had budgeted for the money as I thought I had access to more than 20,000 people and a potential income stream," she said.
"You just don't expect companies to behave like this - what I want to say to them is, you've been trying to lose charities money by doing this. I want to make sure no other charities lose out."
The communications manager at the health trust, who did not want to be identified, confirmed Bird's account to Third Sector. "I'll be listening to what HCC has to say and considering whether we wish to continue with this contract," he said. "To misrepresent potential income to any charity would be quite inappropriate, in my view."