Dr Richard Simpson, a former doctor, said his constituents are confused by the process and it had created a postcode lottery.
He was speaking as an investigation into access to expensive, potentially life-saving medicines opened in the Scottish Parliament.
Scotland has repeatedly been criticised for preventing new, costly drugs from being prescribed by the NHS, when the same treatments are available south of the Border.
The system is led by the Scottish Medicines Consortium (SMC), which advises the NHS on which drugs to pay for after weighing up the benefits against the costs. Regional health boards use this information to decide which drugs doctors can routinely prescribe to patients. Special requests can be made for treatments turned down by the SMC.
The SMC was set up to provide a single source of advice and to help NHS Scotland plan fast and uniform introduction of beneficial treatments.
Dr Simpson said that while the system may work at SMC level, it is "deeply flawed" across the country's 14 health boards, with variations in the drugs available to patients with the same illness or condition, depending on where they live.
"We've got multiple layers of bureaucracy before patients actually receive the medicines," he said.
"The consistency we have across Scotland is if you have your heart attack in the west, you'll get your drug; if you're in the east, you won't. For my constituents it is confusing.
"We have a system that is deeply flawed at that level."
Dr Simpson gave the example of the drug Brilique. It was given general approval by the SMC in April last year but is still not available to patients in Scotland.
"The evidence given to the SMC was that this would save 200 lives each year. So one reaches the inevitable conclusion that the delay of a year or even 15 months in the approval of this drug, because of the bureaucratic process, has actually cost 200 Scots their lives," he said.
The approval process for newly licensed medicines is under scrutiny at Holyrood's Health Committee. During an evidence session, MSPs questioned experts from the SMC and several health boards.
Dr Simpson's concerns were echoed by Andy Powrie-Smith, director of the Association of the British Pharmaceutical Industry Scotland.
He said the UK is 11th in Europe in terms of access to new medicines, with huge variation in the UK between the devolved nations and England, and at health board level within Scotland.
"I think from a patient perspective, that is very hard to justify. So whatever the individual rationale behind different parts of the system, the whole system is making access in Scotland low and slow for patients," Mr Powrie-Smith said.
Figures published yesterday showed some health boards are more likely than others to allow patients to have a treatment rejected by the SMC. In some parts of the country up to 85% of requests are approved, but in other parts half are rejected.
Professor Angela Timoney, chairwoman of the SMC's new drugs committee, told the MSPs: "It is important to remember we spend £1.3 billion a year in NHS Scotland on medicines.
"We would be failing in our duty to the public and patients if there was not appropriate scrutiny of new medicines."
A Scottish Government spokesman said it had already issued guidance to "help health boards make consistent and transparent decisions about the introduction and availability of all newly licensed medicines".