They said evidence points to charges being more effective than discounts in reducing the use of single-use disposable drink cups.
And they suggested introducing a national, mandatory requirement to sell drinks and disposable cups separately, including an initial minimum price of between 20p and 25p per cup.
The report by the Expert Panel on Environmental Charging and Other Measures also recommended banning the sale of non-recyclable expanded polystyrene/PVC beverage cups in line with the EU Single-Use Plastics Directive by 2021.
Ministers will now consider introducing an additional charge to help cut down on the estimated 200 million single-use coffee cups discarded every year in Scotland.
Environment secretary Roseanna Cunningham said: "Disposable cups present an obvious littering issue, but there is ever-growing awareness within our society of the impact single-use plastic has on our wider environment.
"The scale of the issue is also clear - as is the expert panel's conclusion that no one measure alone will be effective: our approach to reducing single-cup use must involve a joined-up effort across government, business, communities and individuals."
The report also recommends promoting recycling and the use of reusable cups.
It is estimated that single-use disposable beverage cups generate around 4,000 tonnes of waste in Scotland each year.
Many disposable cups are made of paper with a waterproof plastic lining, and are difficult to recycle unless they are collected separately from other recyclable material and taken to specialist recycling facilities.
As a result they are often incinerated or go to landfill, creating carbon emissions and contributing to climate change.
The panel said there is "no single solution" to cutting down on the use of disposable cups, and that promoting cultural and behavioural change is critical.
Panel chairwoman Dame Sue Bruce said: "Over the first year the panel has focused its attentions on single-use disposable beverage cups.
"We have discovered that there are many complex issues to tackle and a myriad of factors that must be considered.
"We have asked questions about what we can do together in Scotland - as consumers, communities, producers, retailers and government - to radically change our attitudes and our use of single-use items.
"Our conclusion is that there needs to be a fundamental move away from single-use disposable beverage cups and not just to an improved model for recycling.
"We have recommended a range of measures to achieve this - including charging separately for disposable cups and developing pilots to promote reusable cups."
The Scottish Government said it is already working to improve recycling rates and encourage behaviour change.
Scotland's Deposit Return Scheme will include drinks containers made of Polyethylene terephthalate (PET) plastic - used in plastic drinks bottles - as well as glass, and aluminium and steel cans.
Jenni Hume, campaign manager for the Have You Got The Bottle? campaign, welcomed the "bold" proposals.
She said: "The evidence is that charges and reusable cup systems can encourage both retailers and the public to move away from single-use cups, and the panel's recommendation that polystyrene and PVC cups be banned is also long overdue.
"We would urge the Scottish Government to back these plans as a matter of urgency."