The Scottish Medicines Consortium (SMC) approved Nalmefene, licensed by Lundbeck, after assessing the studies and a positive submission by a charity also funded by the pharmaceutical company.
The revelations have raised questions about whether the health body is scrutinising conflicts of interest.
The SMC has the responsibility of considering whether new medicines should be recommended for use in the health service.
Over £1 billion of the NHS budget in Scotland is spent on drugs every year: a hugely lucrative pot for the pharma industry.
The Sunday Herald recently revealed how dozens of doctors who either sit on the SMC or advise the body have financial links to health firms.
A BBC Panorama investigation tomorrow will also probe the links between doctors and "Big Pharma" at a UK level.
This newspaper can reveal the SMC is facing further scrutiny, this time over the way its recommendations are made.
The SMC last year approved the use of Nalmefene, a tablet used to tackle alcohol dependence by reducing cravings.
It costs around £43 for 14 pills and Scotland was the first country in Europe to prescribe it.
The SMC judgment was based on three clinical trials, which concluded that Nalmefene reduced alcohol consumption.
However, the trials were funded by Lundbeck - the Danish pharma company that holds the licence for the drug. Lundbeck's bid was also supported by the British Liver Trust (BLT), which argued that the pill would provide a treatment option for people with liver disease.
Lundbeck's financial relationship with the BLT is listed on the company's website. It funded a separate BLT report on alcohol reduction to the tune of £6000 in 2012, and provided another £6800 in funding in the same year.
In the BLT's submission to the SMC, six items of funding from pharma companies were declared in the previous two years: £10,000 each from Lundbeck and Janssen; £15,000 each from Gilead, GSK and Pfizer; and £5000 from MSD.
In a recent article for the British Medical Journal, Glasgow GP Des Spence questioned the SMC's decision and queried whether the gains in the Lundbeck studies were "clinically significant".
He wrote: "Who is responsible for interpreting the research in our public institutions, approving drugs like Nalmefene on such questionable evidence? What is the opportunity cost? Surely these resources would be better spent improving alcohol-counselling services?
"The drugs in alcohol addiction have tiny benefits and are a distraction from the real challenges of limiting the availability and increasing the cost of alcohol."
The SMC also made clear that it expected Nalmefene would be prescribed "more commonly" by GPs than in hospitals.
The pharma firm wrote a letter earlier this year to GPs entitled "Helping The Alcohol Dependent Patient Already in Your Waiting Room".
It invited doctors to a briefing on Nalmefene by "leading experts in the field", including consultant psychiatrist Professor Jonathan Chick. Chick had welcomed the SMC decision at the time, saying he was "pleased" Scottish patients would have access to the treatment.
He has provided consultancy services to Lundbeck. Chick did not respond to emailed questions about his work for the firm.
There is no suggestion of wrongdoing on the part of Lundbeck, Chick or the BLT, but the process has raised further questions about the links "Big Pharma" firms have to doctors and patient groups.
David Miller, professor of sociology at Bath University and a campaigner for lobbying transparency, said: "The revelation that patient groups funded by pharma companies are not excluded from the new drugs process only reinforces the need for much greater transparency from the SMC. Declarations of interest must be public, not heard in secret by decision-makers.
"Scottish citizens also deserve much greater transparency from scientists and doctors who are paid advisers to 'Big Pharma'."
Andrew Langford, chief executive of the BLT, said: "We always make an objective decision on whether we make submissions to the SMC or Nice [National Institute for Health and Care Excellence, which is the English and Welsh equivalent of the SMC]."
On the Lundbeck funding, he said: "Unfortunately, because of financial constraints, there are times when we need to get support from the pharmaceutical industry."
An SMC spokesperson said: "All SMC assessments take account of a broad range of evidence. This includes the submission provided by the applicant company, but also involves additional review of the published literature and evidence-based guidelines that are relevant to the medicine being assessed.
"SMC's decision to accept Nalmefene for use within NHS Scotland followed a review of the submission provided by the applicant company and also took account of relevant guidance from Nice and the Scottish Intercollegiate Guidelines Network."