Bahrain is ruled by a Sunni Muslim dynasty, but the tiny kingdom has a large Shia population that has long complained of marginalisation.

"The Special Investigation Unit announced today the conclusion of its probe into the death of a detainee and the referral of the perpetrator, who remains in custody, to criminal trial on charges of assault resulting in death," it said in a statement shared on Instagram.

Authorities were made aware of the death of the detainee, who was not identified, on March 27, through social media and in a report from the general inspector of the intelligence service.

The report showed "the deceased had been detained by the (intelligence) service and assaulted by one of its members, sustaining numerous injuries. He was subsequently transferred to a hospital where he succumbed to his injuries," it added.

The London-based Bahrain Institute for Rights and Democracy (BIRD) NGO on the same day reported the death of Shia activist Mohamed Almosawi, 32, who was arrested at a checkpoint a week earlier.

Authorities said he had been arrested suspected of "espionage" on behalf of Iran.

BIRD said that Almosawi's relatives were told to collect his body from a military hospital and published photographs showing injuries to his body. It called for an investigation into his death.

Human Rights Watch also decried his death and said the body bore visible signs of torture.

Sayed Ahmed Alwadaei of BIRD said o Thursday Bahrain's announcement was "a rare admission of torture by a government watchdog".

But the fate of two other people arrested with him remains unknown, the NGO said, urging the Special Investigation Unit to look into "the status of Sayed Mohamed's co-detainees".

Iran's attacks on the Gulf following US and Israeli strikes and the killing of Iran's Supreme Leader Ali Khamenei, a spiritual leader for many Shias, has stirred tensions in Bahrain.

Since the war began, Bahrain has cracked down on those expressing support or sympathy for Tehran.

Some have been accused of espionage, and more than 200 mostly Shia Muslims have been arrested, according to an AFP report based on interviews with activists and relatives of the detained.

Bahrain has denied cracking down on citizens based on their religious identity.