Goran Lennmarker, president of the Organisation for Security and Co-operation in Europe's parliamentary assembly, said it was "not a fair election" and had "failed to meet many of the commitments and standards that we have".
"The executive branch acted as though it practically elected the parliament [itself]," Kimmo Kiljunen, the organisation's deputy head said, adding the Kremlin had "practically" decided the outcome itself.
Kiljunen was one of 30 deputies from parliaments of 19 European countries in the OSCE who observed the Russian vote.
'Abuse of resources'
Luc van den Brande, who headed the delegation from the parliamentary assembly of the Council of Europe, said there had been a lack of real separation of the branches of power and the vote appeared to be more of a referendum on Putin's policies than a parliamentary election.
He also said there was an "overwhelming influence of the president's office and the president on the campaign" and "certainly abuse of administrative resources" to influence the outcome".
The Communist Party, which trailed far behind with 11.7 per cent of the vote, and only two other parties garnered enough votes to win seats in the State Duma (lower house of parliament).
Seven other parties, including the liberal opposition, failed to cross the seven-per cent threshold for a seat.
The Communist Party rejected the outcome and said it would ask the supreme court to rule on the validity of the vote, citing some 10,000 violations.
End of opposition?
Al Jazeera's Laurence Lee, reporting from Moscow, said: "It's a fairly hardline-looking Russian parliament and clearly one of the things that's happened is the pro-Western, liberal parties have now ceased to exist inside Russia," he said.
"For all the griping from the liberal parties and the Western media about this being unfair - and probably some of it was unfair - Putin enjoys about 80 per cent support among Russians."
Lee also recounted how a pro-democracy youth campaigner he had been interviewing was "physically lifted off the ground by three men who weren't wearing uniform and carted off" when the interview finished.
"You have to wonder why they have to be so heavy-handed with these people when actually they don't pose a threat to Putin's power base at all," he said.
Garry Kasparov, former world chess champion who heads The Other Russia opposition movement, dismissed the elections as a "farce" and "rigged from the start".
The Kremlin hailed the result as a signal from Russian voters that they want Putin to retain influence even after he leaves office.
Putin is required by the constitution to step down as president when his second term ends next year.
Putin said the results were "a good example of the domestic political stability in Russia".
"The legitimacy of the Russian parliament has without a doubt been increased."