The ministry said the first blast happened at 11.30 p.m. local time (6.30 p.m. GMT) by the Iranian embassy, 100 meters from the country's parliament. The second happened 20 minutes later near a charitable foundation run by the leader of an Islamist party, and the third at 8.30 a.m. local time (3.30 a.m. GMT) near the Constitutional Court, about 300 meters from the government building.
No casualties have been reported, although the explosion caused minor structural damage including broken windows in many buildings. The ministry said an investigation has been launched by the country's security service, and that a terrorist attack has not been ruled out.
In a separate incident, a gas pipeline exploded early Friday 20 kilometers (12 miles) outside Dushanbe, the ministry said, leaving Dushanbe and central regions of Tajikstan without gas.
"The explosion was very powerful, and caused a jet of flame about 20 meters high," the ministry press service said, adding that the explosion happened at 1 a.m. local time (8 p.m. Thursday GMT).
Fire-fighters needed five hours to bring the flames under control, the ministry said. It said the flames had still not been put out.