With more than 99% of the ballots counted, Vladimir Putin secured nearly 64% of the vote, according to Russian election officials.
Vladimir Putin told supporters in Moscow he had won in an open and honest battle.
But Golos, a leading independent election watchdog, said the polls could not be considered fair and open.
It said there were instances of forced voting, numerous reports of “carousel” voting – in which voters cast multiple ballots – and that campaigning had been insufficiently competitive.
“Such elections cannot be called fair, just and open according to the Russian constitution and international standards,” a Golos spokeswoman said at a news conference on Monday morning.
Opposition groups have also alleged widespread fraud, and plan a protest rally in Moscow later on Monday.
Tens of thousands of supporters of Vladimir Putin – with Russian flags and banners – took part in a concert outside the Kremlin to celebrate his victory late on Sunday.
Making a brief appearance with current President Dmitry Medvedev, Vladimir Putin thanked his supporters from “every corner” of the country.
“I promised you we would win, and we won,” Vladimir Putin said, his eyes watering. “Glory to Russia!”
“We have won in an open and honest battle.
“We proved that no one can force anything on us.”
Slogans on the banner included “Putin – our president” and “We believe in Putin”.
Vladimir Putin, who supported Dmitry Medvedev in the Kremlin race in 2008 and became prime minister because of a constitutional ban on a third consecutive term as president, will now be in office until 2018. He could then run for another six-year term.
There was tight security around the capital, with 6,000 extra police brought in from outside.
The other three candidates were in single digits.
The turnout is predicted to be about 63%.
After the polls closed, Gennady Zyuganov – the leader of the Communist Party who has previously been relatively loyal to Vladimir Putin – described the elections as “unfair and unworthy”.
But he said that with increasing public anger, Vladimir Putin “would not be able to rule like he used to”.
“These elections cannot be considered legitimate in any way,” said Vladimir Ryzhkov, one of the leaders of the street protest movement, which was not represented in the election.
However, Vladimir Putin’s campaign chief Stanislav Govorukhin described the poll as “the cleanest in Russian history”.
The election was held against a backdrop of popular discontent, sparked by allegations of widespread fraud during December’s parliamentary elections in favor of Vladimir Putin’s United Russia party.
The alleged fraud came despite the presence of thousands of independent observers and web cameras at polling stations.
Opposition blogger and anti-corruption campaigner Alexey Navalny said: “Grandiose scale of falsifications, especially in Moscow… mass use of carousel voting.”
Also on Monday morning, Dmitry Medvedev announced he had ordered a review of the conviction of jailed former tycoon, Mikhail Khodorkovsky.
Mikhail Khodorkovsky, a prominent Kremlin critic who was once Russia’s richest man, was found guilty of embezzlement in 2010 in what many considered to have been a politically motivated trial.
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