Anna Tsivileva will become a new deputy defense minister whose responsibilities will include improving social support and housing for military personnel.
She was a key Russian figure sanctioned by the British government for ties to Putin following his full-scale invasion of Ukraine.
The sackings mark the latest stage of a radical shakeup of ministers launched by Putin in May after he unexpectedly sacked his long-time defense minister Sergei Shoigu.
In April, another former deputy defense minister, Timur Ivanov, was arrested and accused of taking bribes.
Since then, four other top defense officials and general staff have been arrested on the same charges.
The latest reshuffle saw deputy defense ministers Nikolai Pankov, Ruslan Tsalikov, Tatiana Shevtsova, and Pavel Popov removed according to Kremlin decrees.
Replacing them, alongside Tsivileva, is former Deputy Finance Minister Leonid Gornin who has become first deputy defense minister.
Also appointed as deputy defense ministers are Oleg Savelyev and Pavel Fradkov, the son of former Prime Minister Mikhail Fradkov.