Some voters could be forced to travel to two polling stations on the same day, a group that represents constituency returning officers has cautioned.
The warning came as one in three Scots said that they were not confident May’s General Election was well run.
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The Interim Electoral Management Board for Scotland has written to Nick Clegg, the Deputy Prime Minister, and Michael Moore, the Scottish Secretary, to express its concerns.
It warned that running a referendum, which would use Westminster constituencies, alongside parliamentary elections, which would use different Holyrood constituencies, could leave some voters having to cast their vote at two separate polling stations.
Under current law, the elections also have to be treated as two separate polls, requiring two voting cards and two lists of eligible voters, the board also warned.
The letter was revealed just a week after the Electoral Commission warned that combining the two elections was a risk.
Ann McKechin, Labour’s shadow Scotland office minister, said: “Nick Clegg refuses to listen to anyone but himself. It is an act of disrespect not to have even thought about the consequences for Scotland before he announced the date poll.”