"In connection with this, the suspect faces charges ... of negligence leading to the death of two or more people," he said.
The sailor could face up to seven years in prison for his role in the incident, which killed 20 and led to 21 others being hospitalised, Russian news media said.
'No fire aboard'
The authorities said there was no fire aboard the vessel.
An investigation was opened into whether criminal negligence had led to the incident, whose victims included three navy personnel and 17 civilians, many of them shipyard workers participating in the tests.
Independent defence experts alleged that the sailor facing charges may turn out to be a scapegoat for a broader failure.
"It will be absolutely unfair if this sailor is designated the sole person to be guilty of what happened," Alexander Golts, a defence commentator at the Yezhednevny Zhurnal magazine, said.
Pavel Felgenhauer, another defence expert, said: "In Russia there is always a tendency to look for a scapegoat.
"The critical lack of qualified personnel in Russia since the fall of the Soviet Union is the cause of most disasters."
Defective gas masks may also have been responsible for a large number of the deaths on the Nerpa, the Russian tabloid newspaper Tvoi Den reported, citing survivors.
The accident came at a time when Russia has been flexing its military muscle around the world, with Russian warships due to participate in joint exercises with the Venezuelan navy in the Caribbean Sea later this month.
It was the worst naval disaster in Russia since the sinking of the Kursk submarine in the Barents Sea in 2000 in which all 118 sailors on board died.
The Russian military has experienced several accidents in recent years, often related to problems with ageing Soviet-era equipment.