The NHS reimbursed £1.136 billion to pharmacies for prescriptions last year, up 0.9% on the £1.126 billion in 2012, official figures show.
But the number of items dispensed has risen by 1.9%, outstripping the rise in cost and demonstrating value for money, Alex Neil said.
The cost of prescribing methadone alone has increased by almost £4 million, the Scottish Conservatives have highlighted.
Mr Neil said: "During difficult economic times no-one should see cost as a barrier to accessing medical treatment, especially those with long term conditions or cancer who often require a number of prescriptions.
"By abolishing prescription charges in Scotland, this Government has restored one of the founding principles of the NHS - that healthcare is based on clinical need and not the ability to pay.
"The increase in prescribing costs year on year is significantly lower than the year on year increase in prescribing volume, showing that our NHS is continuing to deliver strong value for money and any savings made are being invested in front line services."
Conservative health spokesman Jackson Carlaw MSP said: "The increase in payments relating to methadone is worrying.
"It shows that far from trying to get people off it, too many are being parked on the drug with no proper plan for permanent recovery.
"That doesn't help the individual concerned, and is ultimately of no benefit to the taxpayer.
"Today's figures also show an increase in the number of general prescriptions being given out.
"This is something we predicted, although even we were astonished to find the taxpayer bill rising for items like toothpaste and suncream
"By reintroducing a charge that most people were content to contribute, we'd be able to take the strain off hospital wards by investing in 1,000 additional nurses.
"That would help to create an altogether far better Scottish health service."