"The investigators put Rodchenkov on an international wanted list. Our court on September 21 issued a ruling to arrest him in absentia since he is wanted internationally," the court's spokesperson Yunona Tsareva told AFP.
The move means Russia will be able to request that the United States extradite Rodchenkov, but the two countries do not have an extradition treaty.
The court spokesperson said that Rodchenkov's defence team has appealed against his arrest.
Russian doping: IAAF under fire again
Rodchenkov, 58, is the former director of Moscow's anti-doping lab that oversaw drug testing at the 2014 Winter Olympics in Russia's Black Sea city of Sochi.
He headed the lab from 2006 to 2015 before fleeing to the United States.
In May 2016 he gave an interview to The New York Times describing an elaborate doping scheme that he said involved dozens of Russian athletes at the Sochi Olympics.
A bombshell report by a World Anti-Doping Agency (WADA) independent commission published in 2016 said Rodchenkov had admitted to "intentionally destroying" 1,417 test samples ahead of an audit.
It said Russia's cover-up scheme affected 30 sports and was in operation from 2010 until 2015.
Russia's Anti-Doping Agency (RUSADA) was declared "non-compliant" with international sport's anti-doping code in November 2015 after revelations by Russian athletes in a documentary aired by Germany's ARD television channel.
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Russia's track and field Olympics squad and entire Paralympics team were barred from Rio 2016 and the country remains banned from international athletics.
Russia has consistently denied running a state-run doping programme, with deputy prime minister and former sports minister Vitaly Mutko pinning all the blame on Rodchenkov's laboratory and Russia's Anti-Doping Agency.
"We've acknowledged that this man (Rodchenkov) himself violated all the WADA rules, regulations and standards," Mutko told R-Sport news agency on Monday. "And we've fired him.
The Kremlin has described Rodchenkov as "a person with a scandalous reputation."
The Investigative Committee, which probes serious crimes, opened a criminal investigation into Rodchenkov in 2016, accusing him of abuse of office, for which he could serve up to ten years in jail.
The Russian investigation alleges that Rodchenkov committed violations including destroying samples on his own initiative, in order to conceal errors and keep his job.
They also alleged the leadership of WADA could have ordered Rodchenkov to destroy samples.
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The deputy head of the Investigative Committee Ilya Lazutov said in November that evidence suggested "Rodchenkov for a long time, including for material gain, used his official position to induce athletes to use doping."
Russia has already seized Rodchenkov's assets in the country.
In a New York Times op-ed piece published Friday, Rodchenkov alleged Mutko knew about the doping programme.
"Let me be clear: Mr Mutko knew about and was critical to the success of Russia's doping program... This is a witch hunt, and I am the witch," he said.
Rodchenkov said he fled his homeland because he feared for his life and his family's safety.
"Two days before I fled, a friend within the government warned me that Russia was planning my 'suicide'. I thought that my family might be safer with me gone and, if I were to die, at least I would get to tell the truth to the world first," Rodchenkov said.
He also complained that WADA has not taken sufficient action on its investigation's findings.
A leaked internal WADA report published by the New York Times this month said the agency found it could not gather enough evidence against 95 out of 96 Russian athletes whom it has been probing.
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