The missile, which was being tested yesterday, "deviated from its trajectory and fell close to the little town of Nyonoksa", nearly 1,000 kilometres north of Moscow, the ministry said in a statement.
Investigators are probing the incident.
While there were no casualties, the missile crash did start a fire, damaging all four flats in a two-storey building in the town, according to a source who spoke on condition of anonymity and local media reports cited by TASS news agency.