Subbotin, a former deputy Murmansk governor, won 61 percent of the vote in the runoff election, well over the 35 percent collected by the United Russia candidate, incumbent Mayor Mikhail Savchenko, the local elections committee said.
A senior United Russia official accused Murmansk Governor Yury Yevdokimov on Monday of violating election law by offering support for Subbotin during the campaign and said his party might contest the vote.
"Yury Yevdokimov agitated for votes for one of the candidates on a local channel," said the official, Vyacheslav Volodin, in a statement posted on United Russia's web site.
Volodin said he regretted that Yevdokimov was a party member, and United Russia would review his membership in light of the election.
Yevdokimov dismissed the criticism, saying he did not think that Subbotin's victory would affect United Russia's activities in the region.
Subbotin said Monday that he would not join United Russia, but added that he was a party supporter. "I'm a supporter of Vladimir Putin," he said, Interfax reported. Prime Minister Putin chairs the party.
Still, Subbotin's victory is an embarrassment for United Russia that could lead to a clampdown on outspoken governors, said Alexei Titkov, regions analyst at the Institute of Regional Politics.
"Subbotin's victory will cause temporary problems for United Russia because they will have to explain why their candidate didn't win," he said.
He said United Russia used to give governors more freedoms during elections, but this time it adopted "a very strict position against Yevdokimov, who was not used to it."
A second round of mayoral elections was also held Sunday in Tomsk, Petropavlovsk-Kamchatsky and the Primorye region town of Partizansk. United Russia's candidates won in Tomsk and Petropavlovsk-Kamchatsky.
The party did not back a candidate in the town of Partizansk, and the election was won by independent candidate Alexander Galushchenko, a senior official in the Vladivostok administration.
Local election officials declared an unusually high number of ballots as invalid: more than 25 percent, Interfax reported. Turnout was 25 percent, a large drop from 41 percent on March 1.
The turnout fell after the candidate who led in the first round, Communist Party-backed Vladimir Khmelyov, was removed from the ballot over complaints filed by Galushchenko. Galushchenko ran against incumbent Mayor Igor Rulko, who placed third in the first round.
In Tomsk, United Russia member Nikolai Nikolaychuk was elected mayor with about 51 percent of the vote. Turnout was 43 percent, 6 percent higher than in the first round.
Incumbent Petropavlovsk-Kamchatsky Mayor Vladislav Skvortsov was narrowly re-elected over Mikhail Puchkovsky, who was backed by A Just Russia, another pro-Kremlin party.
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