Estonia's State Assembly passed the bill on a first reading last Thursday, paving the way for dismantling monuments to Soviet soldiers who died liberating the Baltic state from German invaders during the Second World War, but are themselves seen by many Estonians as occupiers.
Estonia declared its independence from the Soviet Union in the early 1990s, and joined NATO and the European Union in 2004.
Speaking to reporters, Federation Council Speaker Sergei Mironov said: "History does not forgive such immoral acts, such moral blunders."
He said the Russian parliament might respond by adopting a special resolution.
Last week, flamboyant ultranationalist lawmaker Vladimir Zhirinovsky, a deputy speaker of Russia's lower house of parliament, suggested severing diplomatic ties with Estonia and imposing an economic blockade on the former Soviet republic.
Zhirinovsky, known for his outspoken statements, said the bill was an attempt to review the outcome of WWII, and that Russia should take a tough line with the "pro-Nazi state emerging on its borders."
The Russian leadership has repeatedly called the EU's attention to Estonia's attempts to glorify Nazi Germany, including with parades by former Nazi SS fighters, as well as to its discriminatory policies vis-a-vis ethnic Russians who moved to the republic following its annexation by the Soviet Union in 1940.
Many members of Estonia's Russian community are denied citizenship and employment rights, and cannot receive an education in their native language.