According to Mikhail Malyshev, only 3 percent chose to restore the 1992 Crimean Constitution and remain an autonomous republic within Ukraine, while 1 percent of ballot papers were declared void.
Voters were asked just two questions on the ballot – printed in the Russian, Ukrainian and Tatar languages – to secede from Ukraine and request annexation by Russia, or to remain part of Ukraine with expanded autonomy for the region.
Malyshev also said that more than 81 percent of eligible voters (over 1.5 million people) cast ballots in the referendum.
Sunday’s referendum is at the center of the most serious geopolitical showdown between Russia and the West since the end of the Cold War.
Ukrainian and Western leaders have denounced the referendum as illegitimate and unconstitutional, while Moscow insists the Crimeans – a majority of whom identify as ethnic Russians – should be allowed to determine their own destiny.
Western leaders have threatened targeted economic sanctions and visa bans against Russian officials responsible for violating the territorial integrity of Ukraine if Crimea secedes and is annexed following the referendum.
The political crisis in Ukraine erupted in November following a step back by President Viktor Yanukovych from closer ties with Europe. Months-long protests in the country's capital Kiev that repeatedly turned deadly eventually led to his ouster by a vote of parliament February 22.
Crimea, along with several other regions in Ukraine, has refused to recognize as legitimate the new leadership in the country.