Janet Waggott the chief executive of Selby District Council, said she would be carrying out a full review over the error which led to the votes wrongly being cast in a by-election for Church Fenton Parish Council in North Yorkshire.
But one local councillor said residents were "livid" at the mistake and that the extra votes case may have made a difference to which parish councillors got elected.
Conservative Richard Musgrave criticised Ms Waggott for knowing that the wrong ballot papers had been cast but declaring the result anyway. But the senior officer said she was obliged to declare the result once a poll has opened and closed.
The confusion occurred on Thursday at the village hall in Church Fenton, between Selby and Tadcaster, which was being used as a polling station for two different elections.
Locals in the parishes of Biggin and Little Fenton were able to cast their votes in the North Yorkshire Police, Fire and Crime Commissioner (PFCC) election, eventually won by Conservative Philip Allott.
But it was also the polling station for votes in the by-election to Church Fenton Parish Council, with four candidates going for three positions.
Coun Musgrave told The Yorkshire Post that two residents of Little Fenton and 18 residents of Biggin who should have been voting for a PFCC were given ballot papers and allowed to vote in the by-election by mistake.
He said: "A number of residents have contacted me to express serious concerns about the conduct of the Church Fenton Parish Council by election last Thursday. It seems that some voters from neighbouring parishes were given the wrong ballot papers.
"Villagers are livid about the situation and I don’t blame them. Democracy is a precious thing and that is why the Returning Officer is given huge resources to ensure that a free and fair election is held. I really feel for the residents involved.
"I have asked the Electoral Commission to carry out a full investigation."
In the end Jessica Kate Cooper, Stewart Keith Ferris and Joanna Louise Mason were elected to the parish council with 259, 267 and 241 votes respectively, while Stuart Metcalfe Spensley missed out with 226 votes.
Turnout was 42.18 per cent from an electorate of 1,048 people.
When approached by The Yorkshire Post, Ms Waggott said: "I have advised the candidates of this issue which was a genuine mistake and have offered an unreserved apology.
"Unfortunately the legal position is such that in the absence of a court order I do not have the power to take action to identify the exact number of additional ballot papers cast. In addition once a poll is opened and closed I am required to count the votes and declare the result.
"I have advised the candidates that they may wish to submit an election petition and that it would not be contested. I will be undertaking a full review of this incident to ensure that improvements are made. I apologise for any inconvenience this has caused."