His party, United Russia, has suffered heavy losses at the polls. The Russian PM has a couple of options now, but they're risky

In one part of Russia, Vladimir Putin got the vote he wanted. In Chechnya, which is under the thumb of a satrap who knows which side his black bread is buttered on, Putin's United Russia got 99.47% of the vote. But it was a different story in the rest of the federation. The party of apparatchiks, hand picked by the Kremlin, limped this morning towards the 50% mark.

With over 96% of the vote counted, this majoritarian party could only muster 49.54%. Each of the Duma's three opposition parties – the communists, the social democrat Just Russia and the ultra nationalist Liberal Democratic party – increased their share of the vote, with 19%,13% and nearly 12% respectively.

This result, to put it mildly, was not in the script dictated by the Kremlin. Putin made no bones about what he wanted. Coming just three months before the presidential one, this election was not about the current limp rag of a leader Dmitri Medvedev, or a tame parliament, or a loyal United Russia. The election was about him: Putin wanted the country to acclaim his place as the country's paramount leader, just before it agrees to elect him for what could be another 12 years of power.

Having forced a ritual humiliation on Robin (to use the cruel metaphor of the US embassy cables) by getting him to stand up in front of the party congress and propose his rival's nomination for the presidency, Batman needed to fly.

Putin needed a thumping majority from the Russian people. He had got rid of political rivals such as the Moscow mayor Yuri Luzhkov because he had made it so abundantly clear that he was the only man in Russia who could do anything. Putin the Action Man – who had himself filmed shirtless on a horse, at the controls of a firefighting helicopter, playing easy rider with bikers, scuba diving for amphora which had been conveniently placed in his path – needed action from the dozy, ungrateful, narod.

He did not get it, or get enough of it. Instead, what he got from an electorate that had to be strongarmed to the polling booths was a clear signal that Russia was wearying of the prospect of another 12 years of this rule. The issue is not the economy, which has been conservatively managed, or pay, which has been increased, or concerns about the stability of the country. Putin has been credited with stabilising the country after the wild 90s when it was almost on the verge of splitting up.

The issues are harder to crack. They are about where Russia goes from here, how it develops as a modern nation, how it will re-industrialise. It is about governing Russia not for the benefit of the elite, but for the benefit of all. It is about social justice, a super wealthy elite, predatory bureaucrats, corruption, the state of hospitals, roads, schools and the general feeling that nothing will really change.

To be fair, this gargantuan task has eluded most Russian leaders throughout history, but even in Yeltsin's drunken days, failure was collectivised. Prime ministers were their own men, with their own cabinets. They could be blamed if things went wrong. Putin is in a different position. He has no one else to blame for his dramatic loss of popularity but himself – precisely because he has made it so abundantly clear that he is the only man who gets things done.

He can now go one of two ways, both of which are not without personal risk. Option one is to become more nationalist and authoritarian. He can rule by fiat. At some point he can even junk United Russia and replace it with another confection of mass support. In the age of freedom of travel, and the internet (albeit one in which opposition websites can be knocked out at a moment's notice, as happened on Sunday), authoritarianism is more difficult to practise. The best and brightest will simply leave, as they are already showing signs of doings. And besides, although he likes to toy with the symbols of the Soviet Union, the modern Russian Federation is nothing like as disciplined or unitary as the communist state was. Russia has much less self-belief and ideology than most western nations.

Option two is to loosen up, become a grandfather figure, choose prime ministers who have really power and responsibility, let real political parties flourish and to live with the consequences of greater democratic pluralism. This, too, is a bear trap. We simply do not know how deep a hole Putin has dug himself into, how much his rule has depended on siphoning public funds for personal enrichment, who pays off whom in the daily ritual of keeping rival business and military clans at bay. We probably never will, but can such a system that is so tightly controlled by a small group of extremely rich and aggressive people – all of whom are in deadly earnest about their keeping their wealth and their loyalty to one man – "loosen up" by letting outsiders in?

In the immediate future the Duma could become at least a more vocal place. United Russia has lost its supermajority power to change the constitution, and will need coalitions to do so. This will make the three opposition parties inside the Duma slightly more likely to oppose Putin. The leader of Just Russia, Sergei Mironov, has some good ideas about how to make the Duma into a real place of debate.

Mironov wants the elimination of United Russia as a monopoly of power; the resumption of direct elections for governors and mayors; the adoption of a law guaranteeing rights to the political opposition; election committees formed from members of each party; the removal of deputies' immunity from prosecution (an important part of the stalled Litvinenko murder inquiry). That is not a bad shopping list of small, but effective measures.

Putin could start to go down this route and still remain president. Whether he will or not is a different matter.

• The first Russian motherboard based on ARM-processor Baikal-M