Popovkin, 50, was tapped to become Defense Ministry's armament chief with the rank of deputy defense minister, ministry spokesman Ilshat Baichurin said, Interfax reported.
Medvedev appointed Oleg Ostapenko to replace Popovkin as head of the Space Forces, Baichurin said.
Ostapenko, 51, had commanded the Plesetsk Cosmodrome, where he had replaced an acting commander fired last year by Defense Minister Anatoly Serdyukov following the beating death of a soldier at the facility.
Ostapenko served as first deputy chief of staff with the Space Forces in 2004 before entering the elite Academy of the General Staff of the Armed Forces.
Popovkin replaces former armament chief Nikolai Makarov, who was appointed head of the General Staff of the Armed Forces last month.
Popovkin's new post is the highest ever occupied by a career Space Forces officer.
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