Russia's Sports Ministry is an "affected party" in the investigation into Grigory Rodchenkov and could sue the former head of the Moscow Laboratory, according to reports.
Russian news agency TASS has said a Moscow Court made the ruling as part of the probe into Rodchenkov, who is facing charges of abuse of authority.
Federal investigators in the scandal-hit nation launched proceedings against Rodchenkov, who turned whistleblower to make sensational claims of systemic illegal drug use by home athletes during the Sochi 2014 Winter Olympics and Paralympics.
His allegations in June included the development of a "three-drug cocktail" of banned steroids which was said to be mixed with alcohol and given to Russian athletes.
"Russia's Sports Ministry has been recognised as an affected party and they are currently preparing to file a lawsuit," an investigator said in the courtroom according to TASS.
It is claimed the Sports Ministry, who were accused of involvement in an institutionalised conspiracy to cheat to win medals at major events, suffered considerable damage as a result of the actions of Rodchenkov, whose testimony sparked the World Anti-Doping Agency (WADA) Independent Commission report into widespread doping in Russia.
The case files also say the Ministry was subjected to a loss of business reputation.
A sizeable portion of land belonging to Rodchenkov has been seized as part of the investigation, as has a home belonging to his daughter Marina Balakina.
Investigators are led to believe the land was bought with money made from the sale of prohibited substances.
The defence claims, however, that there is a lack of evidence and the seizure should therefore be revoked.
The investigation is looking into materials published in some media, where in interviews Rodchenkov alleged many violations of anti-doping regulations in Russian sport, including with his participation.
A further allegation was that a covert system was used to replace the urine of affected medal winners with clean samples, using soda containers and baby bottles to help athletes avoid testing positive.
The Sports Ministry categorically denied Rodchenkov's claims.
A report from Richard McLaren published in December of last year produced evidence that more than 1,000 Russian athletes were implicated in a scheme where samples were tampered with and manipulated at events including Sochi 2014.
Russian officials admit they have doping problems but deny many of the Report's findings.