The result is expected to rely on second choice ballots
Ken Livingstone's campaign manager Tessa Jowell has said she does not think he will win the mayoral race.
She told the BBC: "I think it's highly unlikely that Ken will be mayor of London after the end of this evening."
Results are expected imminently. Tory Boris Johnson leads in eight of the 14 electoral areas on first preference votes, Mr Livingstone in six.
Second preferences have not yet been published. London's Evening Standard says Mr Johnson will not need them.
Ms Jowell said, while it looked like Mr Livingstone would lose, "if you look at Labour's vote in the assembly there are some unexpected surprises there that demonstrate the loyalty of the Labour vote".
She told Sky News later: "We don't quite know the result yet, but we fear that Ken has lost."
The final result has been delayed several times - partly due to increased turnout by voters, estimated at 45%, up from 36.95% in 2004. It could be midnight before the winner is declared.
It follows what Gordon Brown has described as a "bad night" for Labour in local elections in England and Wales.
Johnson: 'A different kettle of fish'
The party suffered its worst council results in at least 40 years and was pushed into third place in terms of vote share by the Liberal Democrats.
BBC research suggests Labour won 24%, the Tories won 44% and the Lib Dems won 25%.
The London election will also decide the 25 members of the London Assembly, which scrutinises the work of the mayor.
Constituency results have started to come in. Labour have held their City and East seat and taken Brent and Harrow from the Conservatives. The Conservatives have held onto Bexley and Bromley and Havering and Redbridge.
Opinion polls had placed Mr Livingstone and Mr Johnson neck-and-neck, with Lib Dem ex-police commander Brian Paddick a distant third.
Livingstone: 'No one can be certain'
Asked if he was encouraged by the Conservatives' performance elsewhere on Friday, Mr Johnson replied: "I think the party's done fantastically nationally but London is a very different kettle of fish and we'll have to see what happens."
Meanwhile Mr Livingstone told reporters he was "feeling fine" and was "just going to sit down and wait like all the rest of you, because none of us can be certain until they announce that result".
The Liberal Democrat candidate Brian Paddick said he had received strong support in Lambeth, where he was a police commander - but he conceded it had been difficult to take on "two giants" who had dominated media coverage.
High profile contest
Speaking at City Hall he told the BBC: "I think we're holding our own, we are coming in around about 15% by the look of things, if we do manage 15% that will be the best performance for a Lib Dem candidate to date."
The race to run London is the highest-profile contest in the 2008 round of elections.
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