The B samples of Olympic short track gold medallist Semion Elistratov and 2015 European short track champion Ekaterina Konstantinova also tested positive.
"The results of the B sample do not change anything for us," Russian Skating Union (RSU) president Alexei Kravtsov told the R-Sport news agency on Friday.
"We are still confident that our athletes are not guilty and we will defend them."
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Meldonium was added to the World Anti-Doping Agency's list of banned substances on Jan. 1.
Kulizhnikov, 21, served a suspension for doping violations between 2012 and 2014 and a second positive test could leave him facing a life ban.
(Reporting by Dmitriy Rogovitskiy, editing by Ed Osmond)
