If confirmed, the result is a considerable blow to Putin because the election was widely seen as atest of his personal authority before his planned return to the presidency next year.
The poll announced on state television showed Putin's party, United Russia, would win the election to the State Duma lower house with 48.5% of the votes cast, compared with 64.3% in 2007.
The poll did not make clear how the 450 seats in the Duma would be shared out under complicated calculations. But a second poll projected United Russia, which has dominated the chamber since 2003, would have only 220 seats.
The communist party emerged in second place in both polls with considerable gains over 2007.
Putin remains by far the most popular politician in the vast country of more than 140 million people but there have been signs that some Russians are wearying of his cultivated strong-man image after 12 years in power.
"United Russia has lost touch with reality," said a 30-year-old history teacher in St Petersburg who gave his name only as Alexander.
He was planning to switch his vote to the Communists.
Putin is still almost certain to win the March 4 presidential election and could extend his rule until 2024 if he wins the maximum two more terms.
The 59-year-old ex-spy looked stern and said only that he hoped for good results for his ruling United Russia party as he walked past supporters to vote in Moscow.
Opposition cries foul
The result was also a blow for President Dmitry Medvedev, who is standing down to allow Putin to resume the presidency he ceded to him in 2008. Medvedev, who would take over the prime minister's office from Putin next year, had led the election campaign.
His position could now be in question.
Opposition parties complained of election irregularities in parts of the country spanning 9,000 km (5,600 miles) and a Western-financed electoral watchdog and two liberal media outlets said their sites had been shut down by hackers intent on silencing allegations of violations.
Sites belonging to the Ekho Moskvy radio station, online news portal Slon.ru and the watchdog Golos went down at around 8am.
"Massive cyber attacks are taking place on the sites of Golos and the map showing violations," Golos said on Twitter.
Medvedev, who is stepping aside next year so that Putin can return to the presidency, has dismissed talk of electoral fraud.
Supporters say Putin saved Russia during his 2000-2008 presidency, restoring Kremlin control over sprawling regions and reviving an economy mired in post-Soviet chaos.
His use of military force to crush a rebellion in the southern Muslim region of Chechnya also won him broad support, and security was tight there on election day.
Opposition parties say the election was unfair from the start because of authorities' support for United Russia with cash and television air time.
Putin has no serious personal rivals as Russia's leader. He remains the ultimate arbiter between the clans which control the world's biggest energy producer.
But his party has had to fight against opponents who have branded it a collection of "swindlers and thieves" and combat a growing sense of unease among voters at Putin's grip on power.
"I shall not vote. I shall cross out all the parties on the list and write: 'Down with the party of swindlers and thieves,'" said Nikolai Markovtsev, an independent deputy in the Vladivostok city legislature on the Pacific seaboard.
Opponents say Putin has crafted a brittle political system which excludes independent voices and that Russians are growing tired of Putin's swaggering image.
Putin is almost certain to win the March 4 presidential election and could extend his rule until 2024 if he wins the maximum two more terms.
But sports fans booed and whistled at Putin at a Moscow martial arts fight last month -- an exceptional event in a country inclined to show respect and restraint towards leaders.