"Of course the Kremlin knows (about the case), the sports ministry gives us information," Kremlin press spokesman Dmitry Peskov told journalists.
"We regret this, but at the same time this situation should not be projected onto the whole of Russian sport.
"The situation should not be presented in such a way that it somehow throws a shadow onto Russian sport, on the magnificent achievements of our athletes."
"We're talking about individual athletes, individual cases."
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The former world number one said a change in the WADA's banned list for 2016 led to an inadvertent violation, for which she will be "provisionally suspended" by the International Tennis Federation.
Sharapova said she originally began taking Meldonium for a variety of symptoms, including a tendency to become ill often, an irregular EKG heart test and a family history of diabetes.
Peskov meanwhile added that Russia's President Vladimir Putin has previously urged the sports officials to look at each doping case "as openly as possible and in full cooperation with the relevant international structures."
"As before we are convinced and consistent supporters of the idea that sport should stay outside politics," Peskov said.
"Attempts to politicise sport, to make sport a political instrument to achieve some aim or other are destructive for sport, for international sport, and are unacceptable and unforgivable," he said.