Russia's President Dmitry Medvedev (L) and Prime Minister Vladimir Putin (R) speak to their supporters in the United Russia ruling party's campaign staff in Moscow.

The poor showing comes after the Russian strongman announced in September he planned to reclaim his old Kremlin job in March presidential polls, reflecting that more and more Russians are growing disillusioned with his 11-year rule.

His party won 49.99 percent of the vote, the central election commission said in results based on 75 percent of polling stations, while the Communist Party was second with 19.35 percent.

The outcome marks a major reversal from the last parliamentary elections in 2007 when United Russia secured a landslide majority of 64.3 percent and won 315 seats in the 450-seat State Duma.

Veteran Communist Party leader Gennady Zyuganov said the vote showed that the Kremlin would have to make more room for the opposition in parliament.

"People have refused to give credence to the authorities, and in the future we will have a dramatically new political layout in the Duma," he said.

Standing alongside President Dmitry Medvedev in an address to supporters at United Russia campaign headquarters, Putin put a brave face on the results.

"Based on these results, we will be able to ensure the stable development of our country," Putin said in a terse speech.

Medvedev rejected the claims of foul play by the authorities, saying the election results showed Russian "democracy in action" and reflected voters' true moods.

Opponents had said the vote was marred by unprecedented violations as the ruling elite downed websites and harassed monitors to limit dissent.

Putin, who has dominated Russia since 2000, is widely expected to win back his old Kremlin job in March presidential elections after his four-year stint as prime minister.

His protege Medvedev is set to step aside and become prime minister, in a job swap that the two men hope will determine Russia's political future and stability for years to come.

The populist A Just Russia group had 12.98 percent of the vote while the ultra-nationalist Liberal Democratic Party was fourth with 11.8 percent, the results showed.

"The authorities are losing trust -- it's a new situation for them," said Sergei Lukashevsky, head of the Andrei Sakharov Museum and Public Center.

"The regime's ideology is exhausting itself."

Maria Lipman, an analyst with the Carnegie Moscow Center, said the ruling party's poor showing will present the Kremlin with a choice. "What to do next?" she said. "To tighten the screws or get adjusted to a new reality in which United Russia no longer has an unchallenged monopoly?"

Moscow Echo radio, citing senior United Russia sources, reported that United Russia chairman Boris Gryzlov would resign his post as Duma speaker, in a sign that the Kremlin will draw lessons from Sunday's vote. The party refused to confirm the report.

Veteran liberal politician Grigory Yavlinsky's Yabloko party trailed in fifth place with 2.89 percent of the vote, insufficient to qualify for seats, the results showed.

Yavlinsky said support for his party was strong in Moscow and Saint Petersburg, where around one in five voted for Yabloko.

Exit polls all showed United Russia winning less than 50 percent of the vote. The state-controlled All-Russian Public Opinion Research Centre (VTsIOM) said United Russia was to win 48.5 percent, ahead of the Communist Party with 19.8 percent.

The four years since the last parliamentary election have been marked by an outburst of criticism of the authorities on the Internet as web penetration of Russia started to finally catch up with the rest of Europe.

Putin was recently subjected to unprecedented booing when he made an appearance at a martial arts fight and opinion polls have shown chinks in his once impregnable popularity.

Independent monitor group Golos (Voice), which claimed rampant violations in the campaign, said its "Map of Violations" website documenting reports of fraud was inaccessible due a cyber-attack and its email was paralysed.

The Communists complained the elections were hit by "mass fraud" that turned them into a "war zone".

The marathon election process in the world's largest country kicked off in Pacific Ocean regions and concluded 21 hours later when polls closed in the exclave of Kaliningrad bordering the European Union, nine time zones away.

Results from Russia's regions showed miserable performances by United Russia, especially in far-flung Primorsky Krai on the Pacific where resentment about the policies of the authorities in distant Moscow is highest.

Police detained around 200 protesters including radical opposition leader Eduard Limonov for holding an unsanctioned protest in Moscow, while another 70 were held at a similar event in Saint Petersburg, police said.