They said Omar Fadhel was killed in the centre of Basra, while at around the same time a key figure in anti-government protests launched in Baghdad in October 2019 was shot and killed by men using a silenced gun as he drove through an eastern district of the capital.
The name of the activist killed in Baghdad was not immediately known.
Fadhel was the first demonstrator killed since October 1 this year, a date that saw the first anniversary of the protest movement and was marked by demonstrators trying to revive their campaign.
Medics said Fadhel was hit by at least one bullet as hundreds of protesters clashed with anti-riot police.
The interior ministry confirmed his death, but said its forces had operated "in conformity with the letter of the instructions" from Prime Minister Mustafa al-Kadhemi, who has repeatedly ordered security forces to avoid the use of lethal force against demonstrators.
Almost 600 people have been killed since October 2019, mostly in clashes with security forces.
The key demand of the youth-led protest movement in the capital and southern Iraq has been the ouster of the entire ruling class, which it accuses of corruption and of being beholden to neighbouring Iran.
Activists have long suffered a campaign of kidnappings and killings to intimidate them into halting demonstrations.
The months-long protest movement eventually lost momentum as tensions between Baghdad's key allies Tehran and Washington spiralled, before demonstrations ground to a halt due to the coronavirus pandemic.
