The PNH Alliance and Rare Disease UK, which had urged reform of the medicine approval system, received financial support from firms that provide drugs in this area.
Since 1999, Holyrood has heard numerous moving accounts of patients being unable to access treatments on the health service. The issue is a key dilemma facing the NHS: patients need drugs, often expensive ones, but the health budget is finite.
The Health Secretary's £21m fund was widely welcomed, as it will undoubtedly benefit some vulnerable patients. However, the revelations have raised questions about how campaign groups are funded.
Until recently, if the Scottish Medicines Consortium, which advises on new medicines, rejected a drug, patients had to make an Individual Patient Treatment Request (IPTR) to an NHS board.
In 2011, bodies including Rare Disease UK and the PNH Alliance (along with PNH Scotland) lodged petitions calling for reform of the SMC and the IPTR system.
In the background section of its petition, the Alliance - which raises awareness of PNH, a rare bone marrow disease - added that the "only licensed and effective treatment" was the drug Eculizumab, whose trade name is Soliris.
Forbes magazine once described Soliris, which the SMC has not recommended for use, as the world's most expensive drug.
The petitions were considered by Parliament's Health Committee, which held roundtable discussions on the wider issue of access to new medicines.
Health Secretary Alex Neil launched a review of the system and last year unveiled the £21m fund for so-called "orphan drugs" for rare conditions, and overhauled the IPTR and SMC processes.
Lesley Loeliger, who co-signed the petition with the Alliance on behalf of PNH Scotland, is a sufferer who has received Soliris since around 2008. She has spoken movingly about her condition.
However, the PNH Alliance is "supported" by a grant from Alexion, the developer and distributor of Soliris.
According to the Alliance website, its secretariat is provided by Advocate, a public affairs consultancy which has declared Alexion as a client. Another petitioner, Rare Disease UK, is listed as a "pro-bono" client of Advocate and is a campaign run by Genetic Alliance UK.
In 2011, RDUK received £50,000 from an "orphans medicines industry group" within the Association of the British Pharmaceutical Industry (ABPI) that included Alexion. Various industry firms also provided £7000 each.
RDUK is listed as the "secretariat and treasurer" of Holyrood's cross-party group on rare diseases.
The sources of funding for the Alliance and RDUK are available on their websites.
Head of the Alliance for Lobbying Transparency, Tamasin Cave, said: "Pharmaceutical firms have long funded patient groups to expressly lobby for policies that benefit their bottom line. No-one would deny sufferers the right to petition government, but bodies like SMC have a duty to make judgments based on evidence and the wider public interest. When funds are tight, special pleading by drug companies should have no part in its decisions."
Opinion is also divided on the value of special drug funds. In 2012, Myeloma UK chief executive Eric Low was quoted by the BBC saying of a cancer drugs fund: "It is often the case that there is not enough evidence to justify the very high prices that drug companies charge for these drugs. In a way, a cancer drugs fund lets drug companies away with that."
Alastair Kent, the director of Genetic Alliance UK, said: "Our finances are completely transparent and open to scrutiny by anyone who wishes to examine them. Rare Disease UK is a campaign run by Genetic Alliance UK, a registered charity which seeks funding from a range of sources."
The PNH Alliance and Advocate did not respond to an email.