An amendment before a committee of the European Parliament in two weeks could prevent UK charities mounting 'on-pack fundraising' campaigns such as those the BHF runs with Findus and Shredded Wheat.
Betty McBride, director of policy at the BHF, said: "This amendment threatens a significant income stream for UK charities. We are working with the Spanish, Netherlands and Slovenian heart foundations to ensure that it doesn't go through.
"On-pack fundraising partnerships are worth more than £1m a year to the BHF. They are clearly marked on pack as just that - generating income to save lives.
"We don't believe customers see these relationships as endorsements.
It is inappropriate for EU politicians to interfere with UK charities in this way."
Draft EU regulations published in 2003 at first proposed to ban all food recommendations or endorsements by medical associations or charities, including the use of logos.
After lobbying by the UK Government, they were amended so that each EU country could draw up its own rules governing recommendations and endorsements.
The Food Standards Agency is planning to consult and draw up guidelines for the UK.
But Renate Sommer, a German Christian Democrat MEP, has tabled an amendment to the revised text that would restore the ban proposed in 2003.
The BHF thinks the amendment, to be debated in committee on 23 March, would end the use of logos in fundraising partnerships. The issue will go to the European Parliament in May.
Sommer, whose party is a member of the Parliament's largest group, has argued that several EU countries have a blanket ban on endorsements and would suffer unfairly if her amendment fails.