The holding will be based on the AirUnion alliance, which was created in 2005. The alliance currently comprises five regional airlines - Siberia's KrasAir, Omskavia and Sibaviatrans; Moscow's Domodedovo Airlines; and Samara, based in the Volga area.
"Appropriate paperwork will be finalized soon," Kirill Androsov said.
An alliance spokesman said AirUnion has yet to become a single legal entity.
"As of now, it is just a technical association of air fleets and air routes. Each company has its own balance sheet and is formally independent," Olga Bykova said, adding that President Putin is expected to sign a decree on the establishment of AirUnion soon.
The ministry said previously a controlling stake (over 50%) in the new holding would belong to private shareholders.
The government currently holds a 51% stake in KrasAir, 50% in Domodedovo Airlines, and 46.5% in Samara, while Omskavia and Sibaviatrans are private companies.
Androsov said earlier the alliance, formed by merging state and private share portfolios, is designed to promote competition on the domestic market.