Speaking at the party's annual congress in St Petersburg, Medvedev said some regional branches of the party did not allow voters to express their will, and he ordered leaders of United Russia to try to win future votes fairly.
United Russia, which dominates Russia's political scene, is led by Vladimir Putin, Russia's powerful prime minister and Medvedev's mentor.
The party, which holds 315 out of 450 seats in the lower house of parliament, has been accused of using its clout to rig procedures to win local elections in October.
Independent observers and opposition parties said the elections were marred by mass violations, including multiple voting and ballot stuffing.
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"Democracy exists not for the parties -- ruling ones or opposition -- democracy exists for citizens in order for the people to be able to use their exclusive right of managing their country," Medvedev said.
"The party is an adjusted tool for that, this is a crucially important tool, but it still is a tool, a means, but not an end."
Putin, who made a speech straight after Medvedev, did not respond to the president's criticism of the party but he warned party members against using United Russia to advance their own career plans.
"I want at the same time to warn those who consider the party to be an elite prestige club membership that would pave one's way for satisfying their personal ambitions and solving their other personal career-related problems," Putin said.
However, Putin said, today "only United Russia is capable" of having "a complete view of problems and to make the right decisions."
Most of Putin's speech focused on the Russian economy and measures to recover from the global downturn and resume growth.
Putin, who hand-picked Medvedev to succeed him as Russia's president in 2008, has not ruled out his own return to the presidency in 2012.
with news agency reports
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