Ken Ritchie, chef executive of the Electoral Reform Society, called for a "full and open enquiry into why so many votes were spoilt in these elections".
The Scottish National party (SNP) made gains in the elections for the Scottish parliament, taking a number of seats from Labour and the Liberal Democrats.
But the vote has been marred by balloting problems as a number of polling centres suspended their counts and the total number of spoilt ballots continued to rise.
It is feared that the number of invalid ballots throughout Scotland could exceed 100,000 and critics, including SNP leader Alex Salmond, have argued that holding Holyrood elections along with local authority elections was too much for voters.
Aside from an unusually high number of spoilt ballot papers, computer system failings in Strathkelvin and Bearsden have meant counts have been suspended.
The problem is replicated in Aberdeen, Eastwood, Edinburgh, Livingstone and Linlithgow and Perth, Argyll and Bute and Tayside North.
Mr Salmond said the election problems were "totally unacceptable in a democratic society" and noted that tens of thousands of Scottish voters had seen their vote discounted.
The SNP leader won his seat in Gordon from the Lib Dems while the party's deputy leader, Nicola Sturgeon, also won the Glasgow Govan seat from Labour.
Nationalists have won seats in Dundee West, Central Fife, Stirling and Kilmarnock, all of which were formally held by Labour.
Tommy Sheridan, who was standing as a candidate for the Solidarity party, lost out on his Glasgow seat and Labour failed to win one seat in the Glasgow constituency.
Scotland's first minister Jack McConnell retained his seat in Motherwell and Wishaw, albeit with a reduced majority over the SNP.
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