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.
Television pictures showed a large fireball and a towering plume of smoke rising up from the outskirts of the city, located about 900 km east of Moscow, the Russian capital.
Sergei Morozov, the governor of the Ulyanovsk region, said: "According to preliminary information, there were 40 people in the workshop, around 35 of which are are currently listed as missing."
But he said the missing were unlikely to be found alive, Russia's Interfax news agency reported.
"In four hours of battling the flames we have not managed to find the 35 people who are missing. The chances are low," Morozov said.
'In control'
Six teams of firefighters were at the scene and were expected to battle the fire "at least until the morning", Russian television quoted Morozov as saying.
"Explosions have practically stopped at this moment. We don't have any particular anxiety so far that we are not in control of the situation," Morozov told television channel Vesti 24.
Sergei Davydov, an aide to Morozov, said only one person had been confirmed injured and had been hospitalised with burns. He had no information on any dead.
The blast rattled windows and set off car alarms in the area and police warned residents to acquire supplies of gauze masks and store drinking water.
Ulyanovsk, located about 900km east of Moscow, the capital, is best known as the birthplace of Vladimir Lenin, the Bolshevik leader.