The discussion document, An Essential Partnership: Principles and Guidelines for Working with Industry, aims to give charities guidelines on entering into collaborations "with clearer expectations and awareness of the issues, and with greater consistency of approach".
The umbrella group's chief executive Simon Denegri said that links between charities and drug companies, which the association describes as "an essential and inevitable aspect of the way medicines and treatments are developed", are on the increase.
"It is important not only that charities are open and transparent about them with donors and the public, but also that they have policies and procedures which underline their integrity and independence," he warned.
The draft guidelines cover a range of topics including intellectual property, sponsorship, campaigning and research. The report predicts there will be more collaborations over drug development in the future because research charities need pharmaceutical companies' expertise in bringing products to the market, while industry can benefit from charities' grass-roots knowledge of patients with particular diseases.
A spokesman for the association denied the document was a "knee-jerk" response to recent controversies regarding charities' links with dugs companies.
Last month National Institute of Clinical Excellence chairman Sir Michael Rawlins said in a speech that charities were in danger of becoming "beholden" to the pharmaceutical industry and should be wary of pharmaceutical donations. His comments came of the back of several incidents in which NICE decisions not to fund certain drugs, such as Herceptin, on the NHS had been attacked by charities and pharmaceutical companies.
The spokesman said the document had grown out of the association's Industry Working Group, which has been in existence since 2006. However, he added: "It takes into account that in recent years there have been occasions where the media has dealt with collaborations in ways which we think have been alarmist. We want this document to encourage collaboration and recognise that it is essential."
Comments on An Essential Partnership: Principles and Guidelines for Working with Industry, available on the AMRC's website, are invited until 1 September. The final version will be published in the autumn.