Unity state almost doublet its record collecting the names of 522,196 voters.
Warrap, Lakes, Northern and Western Bahr el Ghazal and Eastern Equatoria states also registered turnouts well over 100 percent.
Jersa Kide Barsaba Amin from the Southern Sudan High Committee told SCR News that returnees settling in Southern Sudan were the main reason for the increase in voting population.
However, NCP Ibrahim Ghandour told Reuters that there was very clear forgery in most of the registration stations in Southern Sudan.
He added that there has been double registration and underage people were registered and he accused the SPLM of being behind the fraud.
SPLM Secretary General Pagan Amum dismissed the accusation, saying it was the elections commission that carried out the registration, not his party.
Mr. Amum added that the voter registration turnout proves what the SPLM has been saying all along: that the census is wrong.
National Elections Commission deputy chairman, Abdullah Ahmed Abdullah, said the commission is investigating the registration data to find out the reasons for the high turnout.