Russian President Vladimir Putin is to attend the inauguration Thursday of a close ally as Moscow mayor, despite claims of foul play in weekend polls from his anti-Kremlin rival who plans to send a truck-load of complaints to court.

Incumbent mayor Sergei Sobyanin, who barely avoided a run-off in Sunday's closer-than-expected Moscow mayoral polls, will be sworn in during a ceremony attended by hundreds of guests led by Putin on Thursday evening, a Kremlin spokesman said.

The ceremonial swearing-in at one of the capital's landmark parks will take place after the Moscow election commission refused to conduct a partial vote recount demanded by Sobyanin's main rival Alexei Navalny.

Navalny said his team was putting together documented evidence that the vote was partially rigged in favour of Sobyanin, who was appointed Moscow mayor in 2010 but had called the elections before his term was due to end.

According to official results, Sobyanin received 51.3 percent of the vote but Navalny's team insists that the inauguration should be cancelled because, according to its data, the mayor had polled around 49 percent.

Speaking on popular radio Moscow Echo, Navalny said his campaign had prepared more than 950 complaints to contest the vote and would hire a lorry to bring all the papers.

"At 9:00 am (0500 GMT) on Thursday we will submit them to the Moscow city court. We will bring them in a truck: there are 50,000 pages there."

Navalny, who polled a stronger than projected 27.2 percent of the vote, insists that election officials helped the Kremlin ally avoid a second round run-off by allowing irregularities during at-home voting and at polling stations without observers.

The election commission has dismissed the claims and on Wednesday formally registered Sobyanin Moscow's mayor.

In a meeting with Sobyanin and other newly-elected regional chiefs, Putin praised the elections that took place in Moscow and elsewhere across Russia on Sunday.

"The legitimacy of these polls, their transparency, their accountability were on such a level which we have probably never before had in our country," he said.

Independent observers said however they had registered vote irregularities, although not as serious as those witnessed in previous polls.

Widespread claims of wholesale violations during 2011 parliamentary polls prompted tens of thousands to take to the streets of Moscow to protest against the ruling party United Russia and Putin himself.

Analysts say Navalny, who shot to prominence during those protests, was allowed to run in Moscow's mayoral vote to give it a veneer of legitimacy.

Few observers had expected him to poll so strongly, and nearly all pollsters had said he would gain around 20 percent of the vote.

In a departure from tradition, Sobyanin's swearing-in ceremony will take place in a museum at the Poklonnaya Gora War Memorial Park, one of the city's top landmarks.

"They need to cement this victory in a fast and ostentatious way," said pro-opposition political analyst Dmitry Oreshkin.

In the run-up to last year's presidential elections, authorities bussed thousands of people for a pro-Putin rally at the park at the peak of the anti-Kremlin protest demonstrations in the winter of 2011-12.

According to a notice posted on Navalny's blog, a major state company has been told to make sure its employees attend a concert in honour of Sobyanin's inauguration at the park.

Navalny conducted Russia's first Western-style campaign, stumping for votes on the streets and personally distributing campaign literature on the underground rail system.

By contrast, Sobyanin avoided overt political rhetoric, refused to take part in electoral debates and focused his efforts on sprucing up the city.

Analysts saw the election as a key breakthrough for Navalny but also as a sign of an alarming level of political apathy in Moscow, with turnout at just 32 percent.