Mitvol said he had asked the Presnensky Court to order the agency and the Natural Resources Ministry to hold a professional qualification exam to determine which of the agency's four deputy heads should be dismissed.
"The documents have been submitted to the court, and preliminary hearings have been scheduled for November 13," he told RIA Novosti.
Semyon Levi, deputy natural resources minister, signed an order for Mitvol's dismissal in early September, allegedly due to personnel cuts. Three other deputy heads of Rosprirodnadzor kept their jobs.
Mitvol said he is continuing his work for the agency, as the document on his dismissal was signed in the absence of Minister Yury Trutnev, and Levi failed to hand him the document.
In June, Rosprirodnadzor chief Vladimir Kirillov dramatically reduced the role of his outspoken deputy, who had become known for high-profile campaigns against oil companies.
Mitvol was appointed deputy head of the environmental regulator in April 2004, but came to international attention in late 2006 when he led a campaign against oil major Shell that resulted in a lucrative project being sold to Gazprom.
He brought the government's attention to damaging development work being carried out through the Sakhalin II oil and gas project in Russia's Far East, then led by Shell.
He has also spearheaded campaigns over ExxonMobil-led Sakhalin-I, the Kovykta gas field developed by TNK-BP, and a pulp mill next to Siberia's Lake Baikal.
Although in most cases the environmental damage Mitvol has highlighted, including deforestation, toxic waste dumping and soil erosion, has been well documented by environmental groups, the campaigns have often been portrayed in the Western media as part of the Kremlin's drive to bring key oil and gas assets back under its control.
Back in 2005, Mitvol gained publicity within Russia with widely reported cases involving pop diva Alla Pugachyova and electricity monopoly chief Anatoly Chubais over their country estates, which Mitvol said should be demolished because they had been built without planning permission in water-protection zones.
Reports that Kirillov planned to sack Mitvol emerged soon after the new chief's appointment in January this year.
One of Krillov's predecessors, Sergei Sai, tried to dismiss Mitvol in late 2006, but was overruled by the natural resources minister.