“An 18-year-old graduate of this educational institution entered the premises of the Orthodox school gymnasium of the Vvedenskiy Vladychniy convent and blew himself up”, the ministry said in a statement.
A 15-year-old was injured in the attack, which took place in the city of Serpukhov south of Moscow, the statement said.
According to preliminary information, the would-be bomber was not killed in the blast, it said.
The ministry said the staff of the school had been evacuated and that “information about other victims” was being clarified.
Several Russian news agencies said that up to seven people were injured in the attack.
Moscow prosecutors posted a video from the scene of the incident, with police and ambulance cars outside the convent in snowfall.
The incident took place in the city of Serpukhov around 100 kilometers (62 miles) south of Moscow.
The Investigative Committee, which probes major crimes, said it had sent detectives to the scene at the orthodox school.
Russia has seen a rise in teenage attacks on schools in recent years.
In September, a student killed six people and wounded dozens on a university campus in the Urals city of Perm.
In May, a 19-year-old opened fire in his old school in the central city of Kazan, killing nine people.