Periodic outcries over incompetence and corruption at the top of the Russian military have dogged President Vladimir V. Putin’s war effort since the start of his invasion of Ukraine in early 2022.

When his forces faltered around the Ukrainian capital, Kyiv, the need for change was laid bare. When they were routed months later outside the city of Kharkiv, expectations of a shake-up grew. And after the mercenary leader Yevgeny V. Prigozhin marched his men toward Moscow, complaining of deep rot and ineptitude at the top of the Russian force, Mr. Putin seemed obliged to respond.

But, at each turn, the Russian president avoided any major public moves that could have been seen as validating the criticism, keeping his defense minister and top general in place through the firestorm while shuffling battlefield commanders and making other moves lower on the chain.

Now, with the battlefield crises seemingly behind him and Mr. Prigozhin dead, the Russian leader has decided to act, changing defense ministers for the first time in more than a decade and allowing a number of corruption arrests among top ministry officials.

The moves have ushered in the biggest overhaul at the Russian Defense Ministry since the invasion began and have confirmed Mr. Putin’s preference for avoiding big, responsive changes in the heat of a crisis and instead acting at a less conspicuous time of his own choosing.