The prospect of President Vladimir Putin remaining in power for a third presidential term when his current term runs out in 2008 has been widely debated in Russia, although the president himself has repeatedly said he will not run again.
He said the Constitution bans anyone from having more than two consecutive terms as president.
The commission said such a referendum does not comply with the Constitution.
The initiative to hold the referendum came in early September from North Ossetia's civic movement, Accord and Stability.
"Today's decision of the Central Election Commission will be discussed by members of our executive committee, and we reserve the right to appeal the decision," one of the movement's representatives said.
Putin said earlier he was against amending the Constitution to allow a third consecutive term. Another possibility that has been advanced is of Putin taking up the presidency again in 2012, since the Constitution specifies only consecutive terms in office, without imposing a limit on the total number.
"The Russian president is the guarantor of the Constitution, and the president's direct duty is to guarantee its inviolability," Putin told French television channel TF1 in July of this year.
"It is impossible to tie the future of a huge country to the fate of one man, even a man like me," Putin said, adding that running an enormous country such as Russia is a tremendous honor.
Although the next presidential election is scheduled for 2008, media reports have already speculated that Dmitry Medvedev, recently promoted to the post of first deputy prime minister in charge of four multi-billion-dollar national projects to raise living standards, and Defense Minister and Deputy Prime Minister Sergei Ivanov, Putin's former KGB colleague, could possibly be candidates.
Putin said in mid-June the name of his successor will become known as the presidential election draws nearer, but he said it is up to the Russian people to choose a president.
Despite criticism in the West over alleged democratic backsliding, Putin remains hugely popular at home, where he is credited by many for bringing relative order, and for attempts to reconcile the Communists and Democrats following the upheavals of the 1990s.