The Electoral Commission said it would be undertaking a "thorough review" into the chaos and called it a matter for "serious concern".
A spokesman said there should have been sufficient resources allocated to make sure everyone was able to vote.
Chair of the Electoral Commission Jenny Watson was questioned on Sky News about whether she should resign.
She told Sky's political editor Adam Boulton that her commission was not to blame for the mess and that "decisions are made by returning officers who are entirely independent".
She said the law is that doors to polling stations must be closed at exactly 10pm, and that no one may be issued with a ballot paper after 10pm - even if they are inside the polling station.
But Simon Nayyar, Conservative candidate for Hackney South and Shoreditch, said some voters in his constituency were being turned away at 9.15pm because queues were so long.
He said he was "extremely disturbed" by the problems and would be calling for a "full public inquiry".
Voters turned away in Islington, north London
The National Union of Students (NUS) claimed students in some areas had been unable to vote after they were placed in separate, slower queues to other voters.
NUS president Wes Streeting said: "Where students and other voters have been disenfranchised, local authorities should hang their heads in shame.
"It is outrageous that citizens should be denied their basic right to vote and we demand an inquiry into how this situation occurred."
A spokesman for Gordon Brown said: "The Prime Minister is very concerned by the reports and would support a thorough investigation into them."
A Conservative party spokesman said: "These are very disturbing stories which clearly need to be thoroughly investigated."
Asked if the situation amounted to a "scandal", Olympics Minister Tessa Jowell replied: "I think it is.
"These are queues of people exercising their democratic right and then being denied it."