Anatoly Golomolzin said Moscow's forestry regulator had violated anti-monopoly legislation by limiting access to the auctions.
The decision does not automatically mean that the results of the auction will be annulled, but they may be now contested in court, he added.
Sixty-nine forests covering 991 hectares, mostly to the west of Moscow, were offered for rent last December. The auctions were initiated by the federal forestry agency, Rosleskhoz, and organized by Moscow's forestry regulator. The starting price for the plots was under 1,000 rubles ($42.37) per 100 square meters, compared to a market rate of between $5,000 and $10,000.
Auctions for lucrative forest areas have been the focus of attention both in the media and in government bodies of late. An official investigation was concluded in early April. As a result, Moscow forestry chief Sergei Sopin was dismissed.