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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.
"Putin wants to have tighter control on Wagner," says Natia Seskuria, Associate Fellow at the Royal United Services Institute, "to make sure he won't be facing another crisis in the future. It indicates that Putin is becoming more risk-averse."
The decree comes at a time when Wagner mercenary fighters 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 forge the spiritual and moral foundations of the defence of Russia, the wording of the oath includes a line in which those who take it promise to strictly follow the orders of commanders and senior leaders.
"It is a concealed message to military intelligence to find and prosecute Wagner fighters," Petro Burkovskyi, Executive Director of the Democratic Initiatives Foundation, a think tank based in Ukraine, told the BBC.
And it is a clear signal to the fighters, too, he suggests.
"They took the oath in the past as well, it's standard procedure for many armies. So it is a signal to Wagner fighters: Either take the oath and keep your arms or disarm yourself. You obey or you go to prison."
A few weeks before Prigozhin's failed uprising in June, the Russian defence ministry gave mercenary groups until 1 July to sign army contracts.
Prigozhin refused to sign, because he didn't want his Wagner Group to operate under the ministry.
Mr Putin backed the ministry's contract scheme at the time, which was the first public blow against his long-term ally Prigozhin.
But what effect will it have on the Wagner fighters without an obvious leader?
Mr Burkovskyi thinks that as trained and experienced fighters, they are good assets for the Russian army.
"They are mostly career military servicemen, other than being ideological.
"They chose Wagner because Wagner gave them special treatment, without the bureaucracy of the huge Russian army. If they get special treatment under Putin's orders, I don't think they care about where, to whom and for whom they will fight."
Ms Seskuria believes that Prigozhin's real supporters, who don't want to take the oath, might create problems in the long term.
"I think the message is very clear, you either follow the rules or end up like Prigozhin," she says.
"In that sense it will work in a short-term perspective. However, Prigozhin had loyal supporters within Wagner and this can potentially create problems for Putin in a longer term-perspective."
Meanwhile there were drone attacks on Moscow and Belgorod regions on Saturday morning, both shot down by air defence systems, according to Russian officials.
No casualties nor damages were reported. Moscow's three main airports suspended flights for a couple of hours.
In the Belgorod region bordering Ukraine, four people were wounded as a result of shelling, governor Vyacheslav Gladkov said.
Moscow blamed Ukraine for the shelling and drone attacks. Kyiv has not commented yet, as they almost never publicly claimed responsibility for the attacks inside Russia.
And in Ukraine, two people have been killed and one wounded after Russia shelled a Ukrainian village near the northeast town of Kupiansk, Kharkiv's regional governor said, adding that a cafe had been hit.