He said the Navy commander-in-chief Adm Vladimir Vysotsky had ordered to stop the trials and the submarine was heading to a temporary base.
The large anti-submarine ship Admiral Tributs and the rescue vessel Sayany are accompaning the submarine, Dygalo said.
''I declare with full responsibility that the reactor compartment on the nuclear-powered submarine is working normally and the radiation background is normal,'' he said, quoted by Itar-Tass news agency.
He said 208 people, including 81 servicemen were on board the submarine.
He said First Deputy Defence Minister Alexander Kolmakov and Navy commander-in-chief, Adm Vladimir Vysotsky are heading for the site of the accident.
He did not specify the type and name of the submarine.
He said 21 people injured in the accident had been evacuated on board the Admiral Tributs Dygalo said that the accident had not damaged the submarine's reactor.
Russian President Dmitry Medvedev is being kept fully informed about the incident, his press service said.
Russia's worst submarine disaster happened in August 2000, when the nuclear-powered Kursk sank in the Barents Sea. All 118 people on board died.