According to preliminary data, the Communist Party received 11.7%, the ultranationalist Liberal Democratic Party 8.4%, and A Just Russia, led by Kremlin loyalists, gathered 8% of the vote.
No other parties made it past the 7% threshold to gain seats in the State Duma. The Agrarian Party received 2.4% of votes, Yabloko 1.6%, Civil Force 1.1%, and Union of Right Forces (SPS) 1%. The other parties scored less than 1%.
The Central Election Commission (CEC) put voter turnout at around 60%, compared to 55.75% at the 2003 State Duma elections.
An update is expected at 10:00 a.m. Moscow time (7: a.m. GMT)
The CEC said on Monday there was no evidence of violations that could call into question the results of the election.
CEC Secretary Nikolai Konkin said: "So far I see no reasons to doubt the legitimacy of these elections."
He also added that United Russia was expected to take between 310-315 of the 450 seats in the State Duma.
Parties that have cited fraud at the polls must present their evidence to the CEC, he said.
Russia's Communist Party said all other parties that gained seats in the State Duma were mere helpers of the Kremlin, and dismissed the results as rigged.
Communist Party leader Gennady Zyuganov said the LDPR and A Just Russia are "direct helpers and sidekicks of United Russia."
"This is not a parliament, but a branch of the Kremlin, a department of the government," he said.
The Communist Party said it is preparing lawsuits to contest the results of the elections, irrespective of how many seats the party wins.
"The barrage of violations exceeds all acceptable norms," said the head of the party's legal service, Vadim Solovyev.
The leader of the liberal Yabloko party, which failed to garner sufficient votes to enter parliament, said the election was plagued by numerous violations.
"During the voting today every legal statute on voting, without exception, was violated," Grigory Yavlinsky told a news conference.
Speaking after the first partial vote count was announced, the head of United Russia said the party would not use its overwhelming parliamentary majority to force changes to the Constitution.
Boris Gryzlov, who is also the Duma speaker, said that over the past four years the party has used its parliamentary majority to "protect the current Constitution."
He called the result a victory for President Vladimir Putin, who topped the party's candidate list.
Gryzlov conceded that there had been violations in the State Duma elections, but said that these did not affect the result.
The White House urged Russian authorities to look into reports of fraud.
Voting finished at 9:00 p.m. Moscow time (6:00 p.m. GMT), when the last polling stations closed in the westernmost part of Russia, the Baltic exclave of Kaliningrad.
The parliamentary elections were the fifth in Russia's post-Soviet history.
The run-up to the Duma elections was marred by a dispute with the Organization for Security and Cooperation in Europe, after its main election monitoring arm refused to dispatch observers for the polls, citing restrictions and visa delays. Moscow in turn criticized "chaos" in the organization and reinvigorated calls for its reform.