Mikhail Malyshev told a televised news conference that final tally from yesterday's vote was 96.8 per cent in favor of splitting from Ukraine.
He also said that the commission has not registered a single complaint about the vote. The referendum was widely condemned by Western leaders who were planning to discuss economic sanctions to punish Russia.
Ukraine's new government in Kiev called the referendum a "circus" directed at gunpoint by Moscow.
The Crimean peninsula has been seized for two weeks now by troops under apparent Russian command.
Russia raised the stakes Saturday when its forces, backed by helicopter gunships and armored vehicles, took control of the Ukrainian village of Strilkove and a key natural gas distribution plant nearby - the first Russian military move into Ukraine beyond the Crimean peninsula of 2 million people.
The Russian forces later withdrew from the village but kept control of the gas plant. Ukrainian soldiers were digging trenches and erecting barricades between the village and the gas plant yesterday.
The Crimean parliament planned to meet today to formally ask Moscow to be annexed, and Crimean lawmakers were to fly to Moscow later in the day for talks, Crimea's prime minister said on Twitter.