Statistics from the Office of National Statistics (ONS) show that up to 600,000 people could have been missed off the register after comparing numbers to the same period last year.
The statistics, the first since individual voter registration (IVR) was introduced, show a dramatic reduction in the number of young people and people from deprived areas.
The new system has been implemented to try and crack down on voting fraud by making each voter register themselves, rather than the "head" of each household, which previously was responsible for submitting each name.
The ONS results said there were 44,934,029 people on local government election registers and 43,478,635 on parliamentary registers, down by around 1.3% on the last UK figure.
Their results come as a separate study by the Electoral Commission found a total of 770,000 names had been missed off the latest electoral roll.