Gunmen killed a 22-year-old protester near the Bahraini capital early on Saturday, said the main Shiite opposition group Al-Wefaq, blaming militants loyal to the regime.
Ahmad Ismail Hassan was wounded in the stomach when men in civilian clothing fired on protesters calling for "democracy and an end to dictatorship" in Salmabad, on the southern outskirts of Manama, Al-Wefaq said in a statement.
Doctors were unable to save him, it said, adding that "regime militants" carried out the shooting.
The interior ministry said in a statement that the autopsy showed the bullet was not fired by Barhaini forces.
"The first results of the inquiry do not enable us to identify those responsible for the gunfire," it added.
Al-Wefaq's accusation came a week after the group said that a man and a woman died of asphyxiation caused by tear gas grenades fired by Bahrain's security forces to disperse protests in Shiite villages.
On Thursday, hundreds of protesters staged a sit-in outside the offices of the United Nations in Manama demanding action over the "excessive" use of tear gas against demonstrators.
Bahraini police regularly clash with demonstrators who take to the streets in Shiite villages despite a brutal crackdown last year on a month-long protest that demanded democratic change in the Sunni-ruled Gulf kingdom.
According to an independent probe, 35 people were killed in the unrest between mid-February and mid-March 2011.