The Communists, who won 11.6 percent of votes, said they would challenge the result in the courts.
But the head of Russia's Central Election Commission, Vladimir Churov, a former colleague of Putin, dismissed the allegations of fraud.
ENDORSEMENT FOR PUTIN
Financial market analysts said the result was broadly positive, even though it did not give clarity about the big issue of who would succeed Putin and what job the Kremlin chief would take next after he steps down from the presidency.
"For markets, this gives stability for another 12-18 months," said Chris Weafer, chief strategist at UralSib investment bank in Moscow.
Projections by the Electoral Commission showed pro-Kremlin parties would win about 393 of the 450 seats in the next State Duma, the lower house of parliament. That would be more than enough to allow them to change the constitution if they wished.
Putin has not said what he will do after his second term ends in May. Some political observers say he could seek a third term as president, although he has said he will not change the constitution to make this possible.
Opinion polls show Putin, a 55-year-old former KGB agent, is extremely popular after eight years in power. Voters credit him with restoring stability and national pride and like his tough nationalism and criticism of the West.
The international observers said "frequent abuse of administrative resources, media coverage strongly in favour of the ruling party and an election code whose cumulative effect hindered political pluralism" had tainted the election.
In Chechnya, a region in the North Caucasus which faces a separatist insurgency and is run by pro-Kremlin Ramzan Kadyrov, officials said a partial count showed United Russia had won 99.3 percent of the votes on a 99 percent turnout.
Europe's main ODIHR election watchdog -- seen in the West as a key yardstick of the fairness of an election -- decided not to monitor the election, citing obstruction by Russian authorities.
Investors were not overly concerned.
"Criticism over the handling of the election from foreign governments should be short-lived," Weafer commented.
