"I am extremely happy that more than 40 people escaped from that warehouse because they were exactly those people we considered were missing," Sergei Morozov, Ulyanovsk's governor, told state television.
A subsequent report said 11 others were unaccounted for, but Sergei Davydov, an aide to Morozov, said it was possible the missing civilian and military personnel were with relatives.
More than 3,000 people were evacuated from the area following the blasts, which took place while munitions were being detonated in a controlled operation at the city's number 31 arms depot, the Ulyanovsk branch of Russia's FSB security service said in a statement.
Morozov said the fire was out, but that isolated explosions continued late on Friday.
Russia's Interfax news agency quoted the governor as saying six people remained hospitalised.
Several explosions and fires have occurred at munitions storage facilities in the former Soviet Union in recent years.
Ulyanovsk, located about 900km east of Moscow, the capital, is best known as the birthplace of Vladimir Lenin, the Bolshevik leader.