The referendum, was meant to gauge public support for revoking the current constitutional ban on a third consecutive presidential term.
The amendment would theoretically allow Putin to stay in power when his second four-year term expires in 2008.
Several organizations have called for such a change in presidential term limits. The proposal rejected by the Central Election Commission was submitted by a group, called Accord and Stability, operating in the North Caucasus republic of North Ossetia.
Today's ruling appears to leave open the possibility for other political groups to submit similar proposals for a third-term referendum.
Putin has repeatedly said that, in conformity with the constitution, he would not run for a third term.
(Interfax, ITAR-TASS, AP)