Research by The Herald shows that across 25 of the most deprived wards in Scotland, the number of voters aged 18 or over had fallen by more than 5,000 since December 2012 in the days leading up to today's cut-off point for registration.
The Herald's research found there were voter increases in wards in Fife, Edinburgh and Ayrshire, but figures provided for Glasgow showed drops in voter numbers in 13 of its 14 wards.
Sources within the authority said a summer exodus of students may have skewed the figures, and that more than 90 per cent of the city's eligible population were on the electoral roll.
Yes Scotland said the data provided only a "snapshot" of the picture across Scotland. However, pro-UK campaigners and political analysts said the figures would be seen as a blow to the Yes side, following claims that large swathes of disenfranchised voters who rarely vote in parliamentary elections had been signing up to vote in favour of independence.
Polling expert Professor John Curtice also produced a new analysis of the 'missing million', which disputed First Minister Alex Salmond's claim that those who rarely bothered to vote would "play a decisive part in our nation's decision".
Professor Curtice said polls had suggested those who did not vote in the 2011 Holyrood election were more likely to back No, compared to the electorate as a whole.
Speaking about the new figures obtained by The Herald, which were provided by councils and local electoral registration chiefs, he added: "This does not suggest there has been a dramatic upsurge in registration in poor parts of Scotland.
"Clearly, some of the Glasgow figures have been skewed by university students. Leaving that aside, there may have been isolated successes. However, these are extremely unlikely to make
a difference, unless it is an extraordinarily tight race."
The figures show there were 459,253 voters aged 18 or over in the 25 wards, which all had child poverty rates of 30 per cent or higher, according to a study published last year.
The Glasgow figures were current as of yesterday, while the Edinburgh, Ayrshire and Fife areas were a rolling total as of last week. The Inverclyde, Renfrewshire and Clydebank totals were taken from the most recent voting register, which had a cut-off date of August 8. They do not include 16 and 17-year-olds eligible to vote in the referendum. To vote on September 18, voters must register by midnight.
The Radical Independence Campaign has targeted areas of traditionally low turnout in an attempt to sign voters up for the Yes cause. It says its canvassing shows those in poorer areas are significantly more likely to back independence, although they may not be canvassed by official pollsters.
A spokesman for the group said last night: "The independence debate has engaged and given hope to hundreds of thousands of people across Scotland who have been failed by the Westminster establishment for decades. In the last week we have registered more than 1500 new voters."
However, while both campaigns have encouraged voters to sign up, Conservative MSP John Lamont said the figures called the claim "that there were a missing million just desperate to vote for separation" into question.
He added: "Going on this evidence, that was just another misguided ploy at creating the impression the deceitful campaign they have been running is working."
A spokesman for Yes Scotland spokesman said: "The wards selected only provide a snapshot of what is happening throughout Scotland, and represent only about seven per cent of the total number.
"They do not reflect what is taking place throughout the country, where, in Edinburgh and Lothians for example, a record number of residents are now on the electoral roll.
"All the forecasts point to a record turnout at the referendum, but it is still important that everyone who is entitled to vote makes sure they do because this is about the future of Scotland. Everybody who lives and works here should have a say in what kind of country they want for themselves and future generations."
A spokesman for Better Together said: "This is the biggest decision we will ever make as a country so it is important as many people as possible make their voice heard on September 18.
"If we vote for independence there would be no going back, so those who want Scotland to stay in the UK need to get registered and say No Thanks to separation."
Meanwhile, Brian Docherty, chairman of the Scottish Police Federation, has warned politicians and their supporters against using inflammatory language after the No camp expressed fears of "absolute carnage" outside polling stations and said there was a growing atmosphere of intimidation during the campaign.
He said: "Politicians and supporters of whichever point of view need to be mindful of the potential impact of intemperate, inflammatory and exaggerated language, lest they be seen to seek to create a self fulfilling prophecy."