Burundian journalist and AFP correspondent Esdras Ndikumana said he was arrested by government security forces and badly beaten on Sunday at the scene of the assassination of a top general.
Ndikumana, who also works for France's RFI radio, said he was taking pictures at the site of the attack in the capital Bujumbura when he was arrested by members of the National Intelligence Service (SNR) and taken to their offices.
He was held for around two hours, during with he said he was subjected to severe beatings on his back, legs and the soles of his feet.
He was then released and hospitalised, with the injuries also including a suspected broken finger.
AFP's global news director Michele Leridon said she was "very shocked" by the attack.
"We will seek explanations from the authorities in Burundi and an assurance that such an incident will not happen again," she said in a statement.
"Our correspondent must be able to continue to carry out his work in complete safety."
The political crisis in Burundi has seen many independent media outlets shut down and many journalists have fled the country or have gone into hiding because of threats and attacks.
The assassination of General Adolphe Nshimirimana came just over a week after President Pierre Nkurunziza was declared the outright winner of controversial elections, securing a third straight term despite opposition protests and international condemnation.
He was a close aide to Nkurunziza and was widely seen as the central African nation's de facto internal security chief and even considered the regime's number-two.
Nkurunziza's candidacy was condemned as unconstitutional by the opposition and provoked months of protests that left at least 100 dead in a fierce government crackdown, as well as an attempted coup in mid-May.