The disruption came amid a high turnout with some polling stations running out of ballot papers as voters headed to the polls en mass.
David Dimbleby, the BBC’s election night anchor, described the election as a “Third World” ballot.
EC chief Jenny Watson said the system was at breaking point and promised a thorough review into problems around the country, including London, Sheffield, Manchester, Liverpool and Newcastle.
The leaders of the three main political parties have all roundly condemned the situation which led to the chaotic scenes.
Prime Minister Gordon Brown expressed concern at the reports of queues up to two hours long with people being turned away from voting at 10pm, in the face of high turnouts and low staff numbers at polling stations.
His spokesman said the prime minister was “very concerned by the reports and would support a thorough investigation into them”.
David Cameron said a new government must “get to the bottom of what has happened and make sure that it never happens again”.
Liberal Democrat leader Nick Clegg said the situation was simply not acceptable in a democracy.
He said: “It is not right that hundreds later found themselves unable to exercise their vote when the polls closed. That should never, ever happen again in our democracy.”
Ms Watson said that, after carrying out a review, the Electoral Commission would make recommendations to change the law.
She said: “We’ve been calling for better co-ordination, for power of direction for us to tell people what to do, for some time.
“We haven’t been successful in persuading government and parliament to take that up so far.”
The high turnout meant that in some areas election staff ran out of ballot papers.
There were angry scenes at polling stations in Hackney, east London, where would-be voters staged a sit-in after they were told they could not vote, and in Nick Clegg’s constituency of Sheffield Hallam, students tried to prevent ballot boxes being taken to the count after they were turned away.