Rostacom said the accident on Thursday occurred during tests on a liquid propellant rocket engine at the site in Nyonoksa, the BBC reported.
Authorities had previously said that two people had died and six were injured in the blast, including three staff members who suffered serious burns.
The company told the media on Saturday that its engineering and technical team had been working on the "isotope power source" for the propulsion system.
The Nyonoksa site carries out tests for virtually every missile system used by the Russian navy, including sea-launched intercontinental ballistic missiles, cruise missiles and anti-aircraft missiles.
Shortly after the blast on Thursday, authorities in Severodvink, 47 km east of Nyonska, reported a 40-minute spike in radiation, which reached 2 microsieverts per hour, then fell back to the normal 0.11 microsieverts.
Both levels were too small to cause radiation sickness.
However, a local news outlet said that residents in nearby areas rushed to buy medical iodine, with pharmacies' stocks reported to be running out in the cities of Arkhangelsk and Severodvinsk, the BBC reported.
There was a rush on iodine stocks during the 1986 Chernobyl nuclear disaster in Ukraine, which sent a huge plume of radiation across Europe.
The outlet added that medics who evacuated the injured at Nyonoksa wore chemical and nuclear protection suits.
This was the second accident involving Russia's military this week.
On Monday, one person was killed and eight others were injured in a blaze at an ammunition dump in Siberia.
Flying munitions damaged a school and a kindergarten in the area. More than 9,500 people were evacuated.
( With inputs from IANS )