By Gabriela Baczynska and Maria Tsvetkova
MOSCOW (Reuters) - An ally of President Vladimir Putin won Moscow's mayoral election on Sunday, nearly complete results showed, but opposition leader Alexei Navalny's unexpectedly strong showing could alarm the Kremlin and fuel Russia's flagging protest movement.
Early returns allowed Sergei Sobyanin to say he was certain of victory, and results released by the electoral commission after a nearly complete count showed him narrowly clearing the 50 percent barrier needed to win outright.
But Navalny said the results had been falsified and that his campaign team's figures showed Sobyanin had fallen short of the mark in Sunday's voting, meaning the two should face each other in a second-round runoff.
"We do not accept the results that are being announced, and we will not give up a single vote that we received," said Navalny, a 37-year-old anti-corruption campaigner who emerged from a wave of anti-Putin protests as the opposition's leader.
The results put Navalny on 27.3 percent but he said his real support was at 35 percent.
His remarks raise the prospect of a new electoral dispute in Russia after protests stalled last year when Putin, a former Soviet spy who has been in power since 2000, won a third presidential term and took a tough line on dissent.
"It is already clear now that the vote count was conducted with many serious violations, and so we consider the official results of the election to be deliberately falsified," the opposition campaign said in a later statement after the bulk of the results were in.
Candidates from United Russia, which dominates politics nationwide, won most of the more than 7,000 regional and local contests held across Russia on Sunday, but there was another sign of resistance in the big Ural Mountains city of Yekaterinburg where opposition candidate Yevgeny Roizman was on track to narrowly defeat the ruling party favorite.
With more than 99 percent of the vote counted in Moscow, the still preliminary results gave 55-year-old Sobyanin 51.27 percent of votes and Navalny 27.3 percent. Two exit polls earlier had put Navalny on about 30 percent of votes.
A low turnout of around 33 percent helped boost his numbers because the young people who form the bedrock of his support voted in droves and there was less mobilization among elderly, more conservative voters.
Even if Navalny's challenge of the outcome does not succeed, such figures strike a blow for the opposition after a Western-style campaign that appeared to take the Kremlin and Navalny's rivals by surprise with its energy and professionalism.
"We've both voted for Navalny. We like some things about him but first and foremost we really don't like the authorities," said Irina, a woman in her 40s who works in manufacturing and voted with her father.
Several voters who chose the white-haired Sobyanin said they had done so because they had seen improvements in the city since he took office. He has put up buildings and spruced up the city center with pedestrian walkways.
"There is no need for any change, everything is fine here. He's got serious experience now, he's well into this job. I like the way he works and want to see more of the same," said a middle-aged man who gave his name only as Yevgeny.
Political observers say the Kremlin let Navalny run for mayor in the belief that he would suffer a humiliating defeat after being convicted of theft in July and sentenced to five years in prison, pending an appeal.
Allowing Navalny to run - and lose - would have increased Sobyanin's legitimacy, went the argument.
The Kremlin-backed candidate said it had been a fair fight. "We have organized the cleanest, most competitive, most open election in the history of Moscow," he told thousands of supporters around midnight.
In an unusual ruling, a court in the city of Kirov released Navalny on bail the day after he was sentenced to allow him to run in the election in the capital, whose 12 million inhabitants account for more than a fifth of the Russian economy.
A pro-Navalny rally is planned Monday evening on the same Moscow square where he helped lead anti-Putin protests that erupted following allegations of widespread fraud in a December 2011 parliamentary election won by Putin's ruling party.
Navalny aides alleged that Moscow authorities increased the vote for Sobyanin by adding people to voter lists at the last minute and manipulating mobile polling stations designed to let people confined to their homes cast ballots.
Election officials said no major violations had been recorded.
If Sobyanin's first-round win is confirmed, Putin will have a close ally at the helm in Moscow until after the 2018 presidential election, in which the former Soviet KGB spy has not ruled out seeking a fourth term.
Sobyanin, a former head of the presidential administration and ex-governor of Siberia's oil-rich Tyumen region, was appointed mayor by the Kremlin in 2010 for a five-year term.
But he cut his term short and called an early election in a bid to boost his legitimacy and that of the Kremlin, which is trying to strengthen its hold on power after the protests.
Sobyanin is a senior member of the ruling United Russia party, which Navalny has denounced as a party of "swindlers and thieves" - a phrase that caught on over the Internet among opposition-minded Russians.
(Writing by Gabriela Baczynska and Steve Gutterman; editing by Timothy Heritage and Patrick Graham)