Another detainee, Zakaraya Rashed Hassan, 40, had died of sickle cell disease, the ministry added. It was the second such death in a week.
Several Shia activists have complained of being tortured while in custody. The government denies the allegations.
(Warning: Towards the end of the story, there is a photograph of Mr Saqer’s body which viewers may find disturbing).
Bahrain imposed emergency rule last month after weeks of anti-government protests in the tiny Gulf kingdom, where the Sunni monarchy is accused of discrimination against the Shia majority.
The authorities used force to put down the protests, which have left more than 25 people dead.
Rights groups say the government has since detained more than 400 people – including human rights activists, doctors, bloggers and opposition supporters.