President Vladimir Putin has called on all employees of Wagner and other Russian private military contractors to take an oath of allegiance to the Russian state.
The decree applies to anyone participating in military activities in Ukraine, assisting the army and serving in territorial defence units.
He signed the decree on Friday, with immediate effect.
It comes two days after Wagner leaders were presumed killed in a plane crash.
In a separate development on Saturday, a far-right subunit of Wagner, known as Rusich, said it was stopping military operations in Ukraine.
In a Telegram post, Rusich accused Russia's foreign ministry of failing to protect a founding member of the group, Yan Petrovsky, who has been arrested in Finland for visa violations and is facing extradition to Ukraine.
Analysts suggest Mr Putin's decree is part of attempts to reassert his authority following Wagner's mutiny in June.
"Putin wants to have tighter control on Wagner to make sure he won't be facing another crisis in the future," Natia Seskuria of Royal United Services Institute, a London think tank, told the BBC.
The decree comes as Wagner mercenaries are lacking an obvious leader, after a plane presumed to be carrying Yevgeny Prigozhin and other leaders crashed on Wednesday, killing all 10 people on board.
Described in the decree as a step to build the spiritual and moral foundations of Russia's defence, the oath includes a promise to strictly follow the orders of commanders.