"This is unpleasant news," Vladimir Putin's spokesman Dmitry Peskov told journalists.
"We do not agree with this decision, we believe it to be unfair. We denounced and continue to denounce accusations that cases of doping had some kind of state support," Peskov said.
"We are preparing for the Olympic Games," he added.
WADA's decision, taken today in Seoul, raised the spectre of a possible ban of the Russian team from February's Winter Olympics in Pyeongchang.
The International Olympic Committee is expected to decide whether Russia can compete in Pyeongchang at an executive board meeting next month in Lausanne.
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Russia's secret service and sports ministry were accused of orchestrating an elaborate plot that included using a "mousehole" to switch dirty samples at the doping laboratory at the Black Sea resort.
WADA has told Russia to "publicly accept" the report's findings and allow access to urine samples at its Moscow anti-doping laboratory.
Today's suspension was widely expected to be upheld after Russia refused to admit running a state-sponsored doping system.
Following WADA's ruling, the new head of Russia's anti- doping agency RUSADA said today his organisation would continue "the huge amount" of work it has done in recent months.