Patient groups have called for a review of the system which provides drugs not routinely available on the NHS.
Individual Patient Treatment Requests (IPTRs) are used by doctors to obtain medicine which has not been approved by the Scottish Medicines Consortium for the health service.
But charities and campaign groups say the IPTR process can be complex with requirements which are difficult to satisfy for rare medical conditions. They also warn of inconsistent decision-making in different health boards.
Holyrood's Health Committee, which is investigating the issues surrounding access to new medicines, is to hear from several organisations.
In a written submission to the committee, the Paroxysmal Nocturnal Haemoglobinuria (PNH) Alliance, which represents patients with the ultra-rare chronic condition, told MSPs that the Scottish Government must review IPTR referral criteria and ensure that the appropriate expert opinion is included in the decision-making process.
"As a result of the failure of NHS Greater Glasgow & Clyde board to include adequate expert opinion in the IPTR decision-making process, a PNH patient who was not considered eligible for treatment died of severe anaemia caused by his PNH shortly after he received the rejection letter," the submission says.
The Health and Social Care Alliance, a charity representing people with long-term conditions, wrote to the committee recommending "a complete overhaul of the IPTR system".
The alliance said its members highlight examples where people have been discouraged from submitting IPTRs, while others decide against submitting an IPTR "purely because of the nature of the process".
Its submission says: "We would call for greater partnership-working between health professionals and third sector organisations to ensure that everyone with a long-term condition has access to accessible information about the range of treatments that may be of benefit to them and the opportunity to engage in open and honest discussion about these treatment options."
Rare Disease UK wrote to the committee stating that "IPTR referral criteria are extremely difficult to satisfy for orphan medicines and are more likely to result in rare disease patients with the greatest clinical need being refused access to potentially life changing/saving treatments compared to patients affected by more common conditions". The organisation, which suggests a review of the request system, said: "Moreover, in the absence of a recommendation from the SMC (Scottish Medicines Consortium), the reliance on the IPTR process leads to a postcode lottery in access in Scotland."