Russia’s Investigative Committee said Lt Gen Fanil Sarvarov died on Monday morning after an explosive device planted under a car detonated.
Sarvarov, 56, was the head of the armed forces’ operational training department, the committee added.
It said one theory being investigated was that the bomb was planted with the involvement of Ukrainian intelligence services. Ukraine has not commented.
Investigators have been sent to the scene, in a car park near an apartment block in the south of Russia’s capital.
Images from the area show a badly damaged white car with the doors blown out, surrounded by other vehicles in a parking lot.
Since Russia launched its full-scale invasion of Ukraine in February 2022, a number of military officials have been targeted in the Russian capital.
Gen Yaroslav Moskalik was killed in a car bomb attack in Moscow in April, while Gen Igor Kirillov died in December 2024 when a device hidden in a scooter was detonated remotely.
A Ukrainian source later told the BBC that Kirillov was killed by Ukraine’s security service, though this was never confirmed on the record. As a matter of policy, Ukraine never officially admits or claims responsibility for targeted attacks.