Lib Dems would aim to win control of road taxes for Holyrood if that was needed to secure road charging.
Mr Scott said he wanted to replace vehicle excise duty
They would also aim to scrap vehicle excise duty as part of a shake-up of motoring tax, transport minister Tavish Scott told party delegates in Aviemore.
Mr Scott vowed to replace Chancellor Gordon Brown's "blunt motoring taxes" with a fairer system if the Lib Dems won power in Scotland in May.
Whitehall is already considering a UK-wide road pricing scheme.
But it has met with significant opposition from motorists.
Mr Scott last week said quicker progress was needed towards road pricing in Scotland.
The Shetland MSP outlined the party's position on road user pricing to the Lib Dems Scottish conference.
"Gordon Brown penalises motorists across Britain through regressive taxation that does nothing to tackle congestion and hammers the rural motorist," he said.
"So we would replace Brown's blunt motoring taxes with a fairer UK-wide scheme which does what it is meant to - tackle congestion and meet the challenge of climate change.
"It must be revenue neutral and it should mean that in all our built up areas, when there is congestion and we can invest in public transport, we will - to give people the incentive to leave the car at home.
"But where there is no congestion motorists should be better off because in parts of Scotland there is no choice but to use the car."
Although motoring tax is reserved to Westminster, a party spokeswoman confirmed it was prepared to call for power on the matter to be devolved to Scotland.