A Sunday Herald investigation has found numerous cases of charities calling for products to be available on the NHS at the same time as having financial links with the drug firms in question.
The Scottish Medicines Consortium (SMC), made up of doctors and other experts, considers whether newly licensed drugs can be recommended for the health service.
Many of the medicines extend or save lives and are of value to patients, but some are hugely expensive and the SMC must decide whether they are cost-effective.
Patient groups, unlike individual patients, have a special role in the process as they can make submissions to the SMC. However, two former SMC chairmen have expressed concerns about their role.
In a letter to the Sunday Herald, Professor David Webb of Edinburgh University and Professor Kenneth Paterson wrote: "We are enthusiastic proponents of the involvement of patient advocacy groups in the work of SMC and beyond, but share concern that there is a need for greater clarity around the funding, membership and management of such groups.
"Perhaps we need debate as to whether some groups or individuals have interests that make it inappropriate for them to be involved in the decision-making process, or at least to ensure such interests are firmly on the table in discussions."
On this basis, the Sunday Herald examined recent SMC decisions in which patient group submissions were made. A number were made by groups with a financial link - either past or present - to the applicants.
There is no suggestion of impropriety on the part of any of the charities and the financial links were declared to the SMC. However, the revelations have raised questions about the funding of charities and whether there are perception problems with patient groups accepting support from Big Pharma.
Professor David Miller, a sociology professor at Bath University who campaigns for transparency in lobbying, said: "The financial connections between patient groups and pharmaceutical firms give rise to possible conflicts of interest, especially where the patient groups then support the drug with the Scottish Medicines Consortium. The SMC should work towards eliminating advice from patient groups that have potential conflicts of interest."
The SMC accepted this treatment after an application by UCB Pharma UK. It benefits sufferers of active axial spondyloarthritis - one of the symptoms of which is back pain.
The National Ankylosing Spondylitis Society (NASS) told the SMC that Cimzia offered patients an alternative option for this illness. In 2013, UCB Pharma provided funding to NASS to the tune of £26,850.
A NASS spokeswoman denied a conflict of interest and said its position was reached after a consultation with members. The charity's chief executive added that it received no more than 25% of its income from pharma companies, but said she would work to reduce this to 15%.
The SMC approved the use of this gel for acne sufferers following an application by Galderma UK Ltd.
A charity, the Skin Conditions Campaign Scotland (SCCS), argued to the SMC that it avoided the worst side-effects of existing medicines.
According to Galderma's website, the company is one of a small number of "corporate partners" that provides the Campaign with an "annual unrestricted charitable grant". This amounts to £2,000 a year.
The Campaign's Eileen Moulton said: "Our reports to SMC are prepared by volunteer members of SCCS who are independent of pharmaceutical companies and receive no remuneration, expenses, or benefits in kind for this work on behalf of SCCS."
Novo Nordisk recently failed in its bid to have an insulin product for diabetes approved by the SMC, with the medicines body arguing that a "sufficiently robust economic analysis" had not been presented.
As part of the process, the South Asian Health Foundation argued that the treatment may be useful.
According to Novo Nordisk's website, it provided financial support worth £35,000 to the Foundation in 2013 and £12,830 in the previous year.
Dr Kiran Patel, the Foundation's chairman of trustees, said: "The submissions to SMC are made with no influence from pharma companies, who are not involved at any stage in preparation of or submission of statements."
Celgene Ltd's treatment for multiple myeloma - a cancer of plasma cells - in adult patients was accepted for restricted use earlier this year.
The charity Myeloma UK argued that Revlimid, in combination with another drug, reduced the need for hospital visits.
Celgene gave Myeloma UK support of about £108,000 in 2013, and £175,000 in the previous year.
Eric Low, the charity's chief executive, said he understood there was a "perception problem" with patients groups receiving pharma money. However, he said he had been at the "epicentre" of persuading drug companies to reduce their prices, adding that only 5-10% of the charity's income came from pharma.
He said his charity was "above and beyond reproach", adding that it did not depend on industry funding.
Bayer PLC's product helps the visually impaired. The Royal National Institute of Blind People (RNIB) Scotland argued that Eylea was an important alternative to available treatments.
According to Bayer's website, it gave about £97,000 to the RNIB in 2012 and nearly £58,000 last year.
A spokesman for RNIB Scotland said: "Funding from pharmaceutical companies comprises 0.01% of our total turnover. The funding we receive from pharmaceutical companies is for specific projects and we take care there is no direct relationship between a company's product and the type of work our project is involved in."
Merck, Sharp & Dohme Ltd failed to persuade the SMC of a treatment for severely active ulcerative colitis.
The charity Crohn's and Colitis UK made a submission in which it argued that Infliximab may reduce the symptoms of the condition. In 2012, the same charity received about £20,000 from MSD.
A spokesperson for the patient group said industry funding did not exceed 10% of its total income, adding: "We currently take great care to work with a consortia of pharmaceutical companies to avoid compromising the charity's independence. By working in this broad manner, Crohn's and Colitis UK is not closely aligned to any one company.
"All SMC submissions are based around the patient experience and Crohn's and Colitis UK will not collaborate in activities that endorse a specific product or undermine a competitor product."
The SMC agreed to extend the license for this Janssen-Cilag product for treating psoriatic arthritis in adults.
The Psoriasis Association, a charity for sufferers, backed the application.
According to Janssen-Cilag's website, it provided financial help to the charity worth £9,000 in 2012 and £25,636 in the previous year.
A charity spokeswoman said no funding from the pharma firm was received in 2013 or the current year, adding: "Patient support groups declare all conflicts of interest in their submissions to the SMC - not simply involvement with the pharmaceutical company concerned. These are read out to the (SMC) Committee at the start of the public meeting and are available to Committee Members when taking submissions into account."
The SMC recently approved Genzyme Therapeutics' product for multiple sclerosis sufferers.
Two groups - the MS Society and the MS Trust - made submissions in support of the oral treatment.
In 2013, the MS Society received £31,700 from Genzyme, while the Trust benefited from £38,000 of help in the same year.
MS Society Chief Executive Michelle Mitchell said less than 0.5% of the charity's income came from pharma. She added: "We only work with pharmaceutical companies when we're certain it's in the best interests of people with MS. When we do, we're open and honest about it. Pharmaceutical companies never have any influence over the information we provide, the research we fund or our policies, submissions and campaigning in relation to promoting access to new treatments that we believe people with MS will benefit from."
Amy Bowen, director of service development at the Trust, said: "There is no conflict of interest. At the MS Trust we believe that if a drug has been assessed as safe and effective and given a licence, we should do our utmost to ensure it gets a positive appraisal so that it can be funded by the NHS and used to treat people with MS."
The SMC backed this Boehringer Ingelheim drug for patients with advanced lung cancer.
One patient group, the Roy Castle Lung Cancer Foundation, made a submission backing its use.
According to Boehringer's website, the firm gave "donations/sponsorship" worth £16,127 to the charity in 2012, and £400 last year for it to attend the Scottish Health Awards.
A spokesperson for the Foundation said: "Financial support we receive from pharmaceutical-related companies is in the form of specified grants, channelled into events or initiatives that raise public awareness of lung cancer, and to those which aim to improve outcomes for patients and their families. Our submissions to SMC are in no way connected to or influenced by such joint projects and the fact that we declare them publicly shows our commitment to maintaining our impartiality, both ethically and morally."