The blasts - heard across the capital - blew out windows and damaged doors in most buildings at Chelopechene. Traffic was jammed as people fled the danger zone.
Authorities closed nearby Sofia International Airport after debris fell near runways and flights were redirected to Plovdiv, 100 miles (160 kilometers) to the east. The Transport Ministry hoped the airport could resume normal operations Thursday evening.
Some 1,700 of Chelopechene's 2,500 residents were evacuated as a precaution after the blasts. More than 9 hours later, authorities said they could return, but urged caution as unexploded ammunition was scattered all over the village.
The Defense Ministry said nearly 1,500 tons of aging artillery shells, depth charges, grenades and other explosives had been stored at the depots. The communist-era ammunition had been due for disposal by army experts.
The cause of the blasts was not immediately known.
Defense Minister Nikolai Tsonev said there was no immediate danger of new explosions because most of the ammunition appeared to have been blown up. Four soldiers on duty at the depots escaped unscathed, the ministry said.
Environment Minister Djevdet Chakarov said there was no hazardous gas pollution in the region, but dust levels had increased fivefold. A senior presidential aide insisted there was no threat of toxic contamination.
"Large quantities of conventional ammunition are stored in the facility, but there are no toxic chemicals or radioactive substances stored there," said Nikolai Kolev, a former army chief of staff.
Former Defense Minister Nikolai Svinarov said Bulgaria had several similar depots across the country, but said their number and precise contents were "a state secret."
Svinarov said Bulgaria had large quantities of useless munitions left over since its military switched from the Warsaw Pact to NATO in 2004.
He told Bulgarian National Radio the army was unable to immediately destroy all obsolete ammunition due to lack of funds.
