The Scottish Liberal Democrats, who obtained the figures under the Freedom of Information (FoI) law, insist this is "just the tip of the iceberg".
Ten out of 14 health boards across Scotland responded to the FoI requests, which asked specifically about the annual costs of removing and destroying prescription medicines, which are returned unused to pharmacies in their local areas.
The figures showed that the health board which paid the most to dispose of medicines was Glasgow at £120,000.
Among NHS Lothian pharmacies alone, some 44 tonnes of wasted prescriptions were returned in 2011/12.
MSP Jim Hume, the Scottish LibDem health spokesman, said: "Our figures do not show the cost of the medicines that are being wasted or the costs around prescribing them in the first place.
"Many people also throw out unused prescriptions rather than return them to the pharmacy."
"Across Scotland, colossal amounts of medicines are being wasted. Over 80 tonnes of unused medicines were collected from pharmacies in NHS Lothian and Grampian throughout the last year.
"The NHS is facing some of its toughest tests yet with an ageing population and in future years the NHS is going to have to do more with less. We must all do our part to ensure that every penny is used effectively and that wastage is reduced where possible."
In its response, Ayrshire and Arran health board pointed out how community pharmacies used yellow bins for unused medicines.
Last year, 1464 were collected, representing a capacity of around 79,000 litres.
In its response to the FoI request, Lanarkshire health board stressed how it ran regular campaigns to raise public awareness about the waste and cost of unused medicines.
It said: "We have estimated, from national figures and returns to pharmacies, that in Lanarkshire approximately £2m is wasted every year through wasted medicines."
Ayrshire and Arran said it, with other health boards, had run a TV campaign, trying to raise public awareness about unused medicines.