An unidentified gunman fired several shots at Lieutenant General Vladimir Alexeyev, deputy head of the GRU, Russia's military intelligence arm, before fleeing the scene, the investigators said.
Alexeyev's position meant he would have been closely involved in prosecuting Russia's war in Ukraine.
Alexeyev, 64, whose work has been recognised by President Vladimir Putin with a Hero of Russia award, was reported to be in a serious condition in hospital.
Born in Ukraine when it was still part of the Soviet Union, Alexeyev was placed under US sanctions over Russian cyber interference allegations in the 2016 US presidential election.
The European Union imposed sanctions on him over the poisoning of former Russian agent Sergei Skripal and his daughter in the English city of Salisbury in 2018.
Russian Foreign Minister Sergei Lavrov accused Ukraine of being behind the assassination attempt, which he alleged was designed to sabotage peace talks.
There was no immediate comment from Ukraine.
Since the start of the war in 2022, Ukrainian military intelligence has claimed responsibility for assassinating several senior Russian officers, some of whom have appeared on a public list of Ukraine's enemies.
The Kommersant daily, citing law enforcement sources, said Alexeyev's attacker had been waiting when he left his apartment to go to work and that Alexeyev had sustained gunshot wounds to an arm, a leg and his chest during a struggle.
The Kremlin said it hoped Alexeyev would survive and recover.
Putin has been briefed on the shooting and Russia's intelligence services are investigating, it said.
"It is clear that military commanders and high-level specialists are at risk during wartime," Kremlin spokesman Dmitry Peskov said.
"But it is not the Kremlin that should be deciding how to ensure their safety. This is a matter for the special services."
A neighbour of Alexeyev, who gave her name as Alessandra, said CCTV in the apartment building had been working well after unconfirmed reports that the gunman had gained access by posing as a food delivery courier.
Alexeyev's boss, Admiral Igor Kostyukov, the head of the GRU, has been leading Russia's delegation in negotiations with Ukraine in Abu Dhabi on security-related aspects of a potential peace deal.
The latest round of talks concluded on Thursday.
The Kremlin said they were constructive and that talks would continue.
Since December 2024, three other officials of the same rank as Alexeyev have been killed in or near Moscow.
