The MS Society says poor access to specialists as well as a shortage of information and budget constraints mean Scotland is trailing some other parts of the UK in the condition's treatment.
It estimates double the number of people would be taking some kind of medication in Scotland if practice was on a par with the best other areas.
More than 11,000 people are living with MS in Scotland and the country has one of the highest rates of the neurological condition in the world. They say currently about 2500 people are taking some kind of licensed treatment for the condition.
Michelle Mitchell, chief executive of the MS Society, said: "We understand the pressures the NHS is facing, but there are licensed medicines that can transform the lives of people with MS, and it's frankly shameful that they are out of reach for so many."
The MS Society Scotland organised a series of patient focus groups to look at access to medicines last autumn. An interim report on the groups' views says some were deterred from trying new treatments because of potential side-effects but others "had unsuccessfully sought information and advice" about drugs.
Seeing specialists to discuss treatment was also a problem. Some patients said they did not have enough time in consultations to discuss medicines. Others said it was almost impossible to get an appointment because of the length of waiting lists.
Other patients said the costs of medicines meant they were blocked from using them. Two people had been on a treatment called Fampyra, which has been shown to improve walking in MS patients.
It is licensed but has not been brought before the committee that approves drugs for use by the Scottish NHS. The report says though the patients clearly benefited from it, they were refused further funding for the drug.
The report adds: "In one area, NHS managers are believed to be putting pressure on healthcare professionals not to prescribe Fampyra, and clinicians are reportedly now reluctant to put in Individual Patient Treatment Requests."
A spokeswoman for the MS Society Scotland said: "Patients have been through every single hoop to try to get hold of some medicines which could help manage their symptoms, but people are not actually accessing them.
"We have heard from people who have been waiting for over a year, battling with their health board."
The report is issued as a UK-wide campaign called Treat Me Right is launched by the society during MS Week.
A leaflet quotes a Scottish patient as saying: "It took more than a year, two individual patient treatment requests and the influence of my MSP before funding was approved. My mobility regressed and the stress was awful."
The campaign is calling for all licensed MS treatments to be made available on the NHS, for everyone with the condition to have regular reviews with a specialist and to be told about their treatment options.
A Scottish Government spokesman said: "All people living with neuromuscular conditions, including MS, and their families, should get access to high-quality care and support, and access to specialist services when needed.
"We support the aim of the MS Society campaign for MS sufferers in Scotland to have access to medicines approved by the Scottish Medicines Consortium.
"There are a number of medicines available to treat MS in Scotland that are available through a special UK-wide arrangement, and those approved by Scottish Medicines Consortium. Where pharmaceutical companies have not put forward their medicines for approval by SMC this means they will not be recommended for use."