In a statement, the ministry said the strike was intended to derail efforts toward a peace process and fuel an escalation of the conflict.
Governor Aleksandr Bogomaz said six people were killed and 42 others injured in the attack on Bryansk on Tuesday.
According to the statement, 29 people are being treated in hospital.
He did not give any details about the exact location of the explosion.
Ukrainian President Volodymyr Zelenskiy and the Kyiv General Staff said it was an attack on a key factory producing missile components in Bryansk.
Zelenskiy called it a completely justified action while Russia accused Ukraine of deliberately targeting civilians.
According to the General Staff in Kyiv, the Ukrainian army used UK Storm Shadow cruise missiles.
Kremlin spokesman Dmitry Peskov said that demilitarising Ukraine and removing the possibility of such attacks was one of Russia's goals.
He also said on Wednesday that the Turkish city of Istanbul could be the venue for a new round of negotiations between Russia and Ukraine to end the war in Ukraine under US mediation.
All sides are in favour of this, he said.
However, there is no precise information on the date and location of the talks.
Zelenskiy and US Special Envoy Steve Witkoff had recently spoken of considerations to postpone the meeting until next week.
with DPA
