The ministry said on its Twitter account that Saturday’s blast was in the village of al-Maqshaa', along the Budayya highway, outside of the capital Manama.
"Initial inspections uncovered two burnt bodies and a third with burn wounds was taken to hospital," the ministry said.
There were signs the car contained explosive substances, it added.
No further details were given on whether the vehicle had been targeted directly or whether the blast had been accidental.
Witnesses said they heard a loud bang shortly before the car was gutted by fire, and that authorities cordoned off the area.
The Persian Gulf kingdom has been hit by several small bombings in recent weeks as the regime struggled with continued protests.
Bahrain's opposition has been calling for political reforms and an end to perceived discrimination.
Authorities quelled a 2011 uprising that was inspired by Arab Spring protests in other countries, but many areas are still witnessing near daily clashes with police.
On March 14, 2011, troops from Saudi Arabia and the United Arab Emirates invaded the country to assist the Bahraini regime in its crackdown on peaceful protesters.
Local sources say scores of people have been killed and hundreds arrested since the start of the uprising.
Last month, Amnesty International censured Bahrain’s “relentless repression” of anti-regime protesters, saying Bahraini security forces “repeatedly” use “excessive force to quash anti-government protests.”
NTJ/HH