The joint venture, to be named Moscow NPZ Holdings B.V., would be formed by transferring 90.02% of the Moscow Oil Refinery's voting shares to the JV's authorized capital.
The federal agency said all parties concerned may present any data "on the impact of the proposed merger on the status of competition" in the sector.
The two companies said they are also planning to merge other Gazprom Neft and MNGK assets on a mutually beneficial basis.
MNGK holds a controlling stake (50.84%) in the Moscow Oil Refinery, which owns 139 filling stations in Moscow and the area around the capital. Sibir Energy plc, in which the Moscow city government has an 18% stake, holds 100% in MNGK.
The Moscow Oil Refinery has capacity to refine over 25,000 million metric tons of oil a day.
Gazprom owns a 75% stake in Gazprom Neft, known as Sibneft before it was taken over by the energy giant in September 2005, while another 20% belongs to a consortium of Italy's ENI and Enel.
