Tourism Secretary Fergus Ewing said that increases in air passenger duty (APD) rates since 2007 and those projected through to 2016 are estimated to result in a loss of £2.1 million passengers to Scotland's main airports per year on 20 November 2012.
Mr Ewing said that it "really is a shocking statistic" and "we really cannot afford to suffer losses of that order".
Scotland's three largest airports have called on the chancellor to conduct an urgent review of air passenger duty.
It follows a report commissioned by Aberdeen, Glasgow and Edinburgh airports which claimed the tax could cost Scotland more than two million passengers a year by 2016.
It also warned the move could cost the Scottish economy £210m a year in lost tourism spend.
At decision time MSPs voted 93 to 19 with one abstention in favour of theScottish Government motion noting "with concern" the recent report by York Aviation on the impact in Scotland of rises in the UK Government's air passenger duty (APD).
During the debate, Mr Ewing called for APD to be devolved so that the Scottish Government could set a more competitive rate.
He said the "Scottish government has been clear that the devolution of APD should take place as soon as possible".
Labour MSP Richard Baker said that "A passenger flying from London direct to Orlando from Heathrow will pay APD once. A passenger flying from Aberdeen to London and then to Orlando will pay APD on both journeys."
"We see that as clearly unfair."
Conservative MSP Alex Johnstone said there was no guarantee that a future Scottish government would not increase APD if the powers were to be transferred.
He said "Then there is the simple fact that the reduction or abolition of this tax in Scotland alone would only ever have a marginal effect in comparison to reducing or abolishing that tax on a UK-wide basis."
Scottish Liberal Democrat Leader Rennie said he did not agree there was any evidence "that taking APD levels and freezing them, or taking them back to 2007 levels will suddenly have a return of 2.1 million passengers".
However he said on a note of consensus "we do believe that APD should be devolved. We have stated that for a long time".
Green co-leader Patrick Harvie said the reality was that "a reduction on APD is regressive".
Mr Harvie said it was the wealthiest who flew most and they would be the ones to save money.