Pharmacists have denied taking millions of pounds of NHS money in the sale of overpriced drugs.
The total Scottish drugs spend is about £800m a year
Documents leaked to a Sunday newspaper claimed to show profits on some treatments of up to 400%.
The industry denied profiteering and a spokesman insisted pharmacies had saved the NHS more than £100m by driving down the cost of drugs.
The Scottish Executive said there were periods when new drugs to the market could show "volatile" price variations.
One treatment for gastric problems, Omeprazole, can be bought from wholesalers for between £2.50 and £3.40, yet the NHS pays £10.85 every time it is prescribed.
Figures in the documents obtained by the Sunday Times claimed to show other profit margins ranging up to 400%.
Buying in bulk on special deals drives down wholesale prices and pharmacists insist these savings are passed on to the NHS.
Frank Owens, from the Scottish Pharmaceutical General Council, said: "We acknowledge that discounts do exist and the Scottish Executive are well aware that those discounts exist.
"But it's those same discounts that actually save NHS Scotland well in excess of £100m per annum in the drug bill."
This year the NHS overspend is likely to be about £81m.
The Scotland's Patients' Association has called for profit margins to be lowered.
The group's Margaret Watt said: "We're quite comfortable with a 5% or 10% mark-up," she said.
"We're certainly not comfortable with 400%, we do believe that this money should be used in the NHS to help the NHS.
"After all at the end of this year, this financial year, I'm quite sure it's going to be in a deficit."
Start-up costs for a chemist can reach £500,000 and pharmacists say the prices have to reflect their costs.
A spokesman for the executive said NHS Scotland did benefit from allowing the market to find its own level.
He said: "In the early months after a drug loses licence protection there is scope for significant volatility in the market as new suppliers of generic equivalents enter the market, and the average market price steadily falls.
"There may be particularly wide short-term variations in the market prices on particular products, although eventually the market stabilises at a level where NHS Scotland is achieving very significant benefits by comparison with the costs of the original licence protected products."