The 2007 Scottish elections were memorable for many things. Unfortunately, one of these things is the fiasco of the rejected votes. Many thousands of voters found yesterday that they had been disenfranchised in the Scottish parliamentary elections because they had failed to get to grips with the complexity of a new ballot process. It was not straightforward, compared with the traditional method of voting under a universal first-past-the-post model. If we want elections to be fairer, by making as many votes as possible count, and if we are committed to boosting participation in an age of apathy, we have to find new ways of organising ballots. Democracy suffers unless these two goals are advanced.

Scotland embarked on a path to deliver these goals when proportional representation was introduced for the first Holyrood elections in 1999. Most voters were familiar with PR for electing MSPs on the regional lists by the second elections in 2003. A lot changed in Thursday's elections; too much, it transpires. It is a matter of great regret (not to say some shame) that the partial failure of the system has diverted attention from a truly engrossing contest that left the SNP as the biggest single party in the parliament's third term.

Will Alex Salmond, the party leader, seek coalition partners to form an administration with barely a working majority or will his party go it alone? How will the pro-Union parties respond? Will they try to coalesce to block the SNP? Is a period of prolonged political instability, marked by a minority SNP government being voted down at every opportunity, the likely outcome? Those who prefer a settled outlook might not approve, but there is no denying that Scottish politics just got a whole lot more interesting.

But there is an impediment to hitting the ground running that will undermine democracy in this country until it is eradicated.

Douglas Alexander, the Scottish Secretary responsible for the Holyrood elections, has already announced that the Electoral Commission's (EC) routine review of the poll and the council ballot will be widened to encompass failures in the delivery of postal ballots and the confusion that caused so many voters to fill in papers mistakenly and, as a consequence, be disenfranchised.

Given that the EC is part of the process, is it right that it should be given the role of leading an investigation when it will, to a degree, be scrutinising itself? The answer is no. This matter is so grave that nothing short of an independent judicial inquiry, of the type demanded yesterday by Mr Salmond, will suffice. It should go without saying that the investigation has to be independent, with powers to call witnesses whether from the spheres of politics, officialdom or business. Politicians have a habit of seeking to lay the blame elsewhere when something they have been involved in goes wrong. An independent inquiry should ensure that this does not happen, and that the truth will out. Having identified the causes, it can then publish recommendations to ensure that there is no recurrence.

Several questions need to be answered. Was the demand for postal ballots underestimated? How, when evidence shows it has become an increasingly popular option with the electorate? If there was an underestimate of demand, who was responsible? What went wrong with the electronic count in those constituencies where returning officers and their staff had to postpone results until systems worked? Was sufficient attention paid at a political level, at Holyrood as well as Westminster, to concerns expressed by those who argued that asking the public to vote in three different ways, on two different voting papers, on the same day was asking too much? We can already guess the answer to the last question: no. Scant attention was paid to the doomsayers, notably the Scotttish Senior Citizens' Unity Party (SSCUP). Hindsight demonstrates it had good cause to raise objections. It appears that older voters had most trouble with the changes. Paradoxically, the body of voters that does most to stop turnout falling further, by bothering to exercise the vote, seems to have been disproportionately disenfranchised. Is it more than coincidence that the SSCUP is no longer represented at Holyrood? Other bodies expressed reservations about rolling the three ballots together. The Arbuthnott Commission on addressing apathy recommended splitting the Holyrood and council votes.

The EC and returning officers advised delaying the count for all three to give the technology time to prove its worth. But the politicians pressed on and the result of thinking that they knew best is there for all to see: a tarnished poll; another cloud over Holyrood after the cost of the parliament building; and the possibility of legal action on the part of minority parties to reclaim votes whose loss they suspect cost them seats. It does not constitute the auspicious start for the next phase of our evolving, maturing parliament we had hoped for.

This is not to suggest that change is bad. It is good when it encourages people to vote, makes their vote tell and, in an efficient manner, provides accurate results promptly. Ministers intended that the voting and counting system they opted for would do all three. In the event, it did none. It has also become clear that, despite the expenditure of significant sums of public money, the linked messages to vote, and how to exercise the vote, did not reach enough people. We need to go back to the drawing board if we are to impart these messages effectively.

When the bill to introduce the STV form of PR for council elections was published late in 2003, The Herald commented: "There are . . . compelling reasons for extending STV beyond council elections. Stopping there would mean that Scots would be faced with four systems when going to the polls . . . If voter apathy is to be tackled, the electorate needs clarity and simplicity, not the confusion and complexity likely further to depress turnout."

That statement is as true today as then; truer, and more telling, because of the blights on the 2007 poll.