Moscow (CNN) -- Russian Prime Minister Vladimir Putin appears to have suffered a serious setback in parliamentary elections over the weekend, slimming his party's majority and political clout.
With 96% of the votes counted, Putin's United Russia party took the largest share of the vote in Sunday's elections with 49.5%, followed by 19.2% for the runner-up Communist Party, according to the Central Election Commission's website on Monday. The Fair Russia party had 13.2%, and the Liberal Democratic party had 11.7%.
But the numbers add up to a significant loss. United Russia stands to lose many of the 300 seats it currently holds in the 450-seat Duma -- Russia's parliament -- possibly shedding more than 60.
It looks set to lose the power to change the constitution unopposed, said Maria Lipman of the Carnegie Endowment for International Peace in Moscow.
"The Kremlin was used to having a monopoly of decision making, but no longer does," she said. "It looks weaker."
The setback was partly the result of educated, urbanized voters deciding they'd had enough of rigged elections, she said.
"People who would have stayed home, assuming the elections had preordained results, rushed to the polls to try to undermine United Russia's showing," she said, tearing their ballots, scribbing on them, or "voting for any party on the ballot whether they felt attracted to it or not."
But she said the "groundswell of defiance in the last days before the poll" was more a mood than a movement.
"These voters do not have a party, do not have a voice that represents them, do not have a leader," she said.
The key question now is how Putin -- who is due to run for president early next year -- will react, Lipman said.
"By far he is the most popular politician in the country but the trend is negative for him," she said.
His options include cracking down on opponents, launching a charisma offensive, reshuffling his cabinet, or liberalizing, she said -- but she held out little hope he would take the last course.
"I find liberalization highly unlikely," she said, calling it "an admission that he should yield control."
"Life is no longer easy for him. He no longer has a constitutional majority," she said.
But President Dmitry Medvedev, who headed the United Russia ticket, said the party made a "decent showing," and that "the result of these parliament elections reflects people's attitudes"
"United Russia remains the leader and the largest political force elected to the parliament," Medvedev said at his party's headquarters. "The party has proven it has a moral right to continue the chosen course."
Putin, who spoke after Medvedev, thanked those who voted for his party "despite the difficulties, despite the economic crisis."
"Based on this result, we will manage to ensure the stable development of our state," Putin said. "I would like to thank everybody who facilitated this result."
Analysts had anticipated Putin's party would win less support than four years ago -- but would still maintain a majority. With three parties not receiving enough votes to take a seat in parliament, as the opinion poll indicates, then United Russia could still hold on to majority.
The developments came as around 100 protesters were arrested in Moscow Sunday, according to official news agency RIA Novosti, citing police. Authorities detained 70 more in St. Petersburg. Police had warned protesters earlier in the day not to hold "unsanctioned rallies" in Moscow, the Interfax news agency reported.
Opposition websites, radio stations and an election monitoring group claimed they had come under online attack.
The Golos election watchdog organization said callers reported about 1,000 elections violations on a telephone hotline, while its website was under attack. Russia's Interfax news agency reported that several other radio and newspaper websites had reported attacks.
The allegations came as voters cast their ballots in polls for the State Duma, the lower house of Russia's parliament.
Putin, recently tapped by his United Russia party to be its presidential candidate next year, has accused the West of trying to influence the elections.
In campaigning ahead of the vote, opponents accused the ruling party of corruption and nepotism, RIA Novosti reported.
Putin said last week that his party had earned the support of "every thoughtful, objective, serious person who wants a better lot for himself, for his children and for Russia," the news agency said.
Russia's Interior Ministry opened three criminal cases and reported hundreds of other "electoral breaches," RIA Novosti said.
Moscow police said they detained about 12 people who were distributing political leaflets -- a practice banned on election day.
Golos said there was increasing pressure at the local level to block observers from accessing polls.
"It is clear that these actions are taken by authorities to undermine the achievement of our long-term goal -- to make the elections in Russia free and fair by impartial and independent monitoring," the organization said in a statement.
In a taped interview with Russia's national TV networks in September, Medvedev criticized allegations that Russia's elections had a predetermined outcome.
"I consider such statements absolutely irresponsible, deceitful and even provocative," he said.
Also in September, Medvedev called on the United Russia party to endorse Putin for president in 2012. Putin, in turn, suggested that Medvedev should take over the role of prime minister if the party wins elections in what would be a straight swap of their roles.
Putin stepped down as president in 2008 because the Russian constitution at that time limited the office to two consecutive four-year terms.
Under amendments to the constitution that went into effect on December 31, 2008, the presidential term was extended to six years.
This means that if Putin is elected in March 2012 for six years, he would be eligible to run for another six-year term after that, potentially keeping him in charge until 2024.
CNN's Alla Eshchenko, Natalie Allen and Maxim Tkachenko contributed to this report.