It gave no details about the death, saying only that his burial would take place on Wednesday in the central town of Tanghin-Dassouri.
Local inhabitants speaking on condition of anonymity said Kabore was kidnapped on Monday after his car was stopped by armed men near Karo as he was heading to Tcheriba, where he was also mayor.
A colleague of Kabore and his driver were able to escape, but the prefect was later found dead in a nearby forest, security sources said.
Last month, the army said it had carried out a security sweep in the region, mobilising more than 800 soldiers and members of the VDP volunteer militia.
One of the world's poorest countries, the landlocked Sahel state has been ravaged by a jihadist insurgency that swept in from neighbouring Mali in 2015.
Around 10,000 people have died, according to an NGO estimate, while around two million people have been displaced and more than a third of the country lies outside the government's control.
Anger at failures to roll back the rebels sparked two coups last year that led to the ascent of the current junta leader, Captain Ibrahim Traore.
He has vowed to reconquer lost ground, but attacks this year have claimed hundreds more lives
Abducted Burkina Official Found Dead
OUAGADOUGOU - Amadou Kabore, the prefect - the highest representative of the state - in the Boucle du Mouhoun region, died on Monday, the ministry of territorial administration and security said in a statement.
