At a massive rally just outside the Kremlin, Putin thanked his supporters for helping foil plots aimed at destroying Russia, sounding a nationalistic theme that has resonated with the prime minister's core supporters.
The win, however, was tainted by claims of violations, including "carousel voting," where voters were bused around to cast multiple ballots.
Putin tallied 58-59 percent of the vote, according to exit polls cited by state television. The Communist Party candidate, Gennady Zyuganov, was trailing far behind Putin with some 18 percent, according to the exit polls. The others - nationalist Vladimir Zhirinovsky, Sergei Mironov of the socialist Just Russia party and billionaire Mikhail Prokhorov - were in single digits.
Official vote results from far eastern regions where the tallying was already done seemed consistent with the poll data. With just over 14 percent of all precincts counted, Putin was leading the field with 62 percent of the vote, the Central Election Commission said.
However, if claims of voting violations are confirmed, they could undermine the legitimacy of his victory and trigger protests. Golos, an elections watchdog in Russia, said it received numerous reports of carousel voting.
Evidence of widespread vote fraud in December's parliamentary election drew tens of thousands to protests against Putin, who was president in 2000-2008 before moving into the prime minister's office due to term limits. They were the largest outburst of public anger in post-Soviet Russia and demonstrated growing exasperation with massive corruption, rising social inequality and tight controls over political life under Putin.
Putin has promised that the vote would be fair this time around, and authorities have tried to appease protesters by allowing more observers to monitor the vote. Tens of thousands of Russians, most of them politically active for the first time, had volunteered to be election observers, receiving training on how to recognize vote-rigging and record and report violations.
Golos said there have been fewer obvious violations than during the December election, but they still believe that violations are extensive. This time, election officials are using more complicated and subtle methods, said Golos deputy director Grigory Melkonyants.
The Associated Press contributed to this report.