The convoy was on a marathon trip to resupply French troops in Mali when it was first stopped and stoned by demonstrators at Kaya in the centre of Burkina Faso.
The convoy then crossed into Niger but was blocked again at Tera in the west of the country, where three people were killed in shooting blamed on Nigerien or French troops.
In December, Nigerien President Mohamed Bazoum ordered an inquiry into the incident and called on France to do the same.
"The results of the investigations by the Niger gendarmerie and the French army having been unable to determine the precise sequence of events which led to deaths and injuries among the demonstrators, Niger and France have decided to jointly compensate families of the victims and the wounded," the Nigerien interior ministry said.
The two countries will "equally share" compensation, it said in a statement late Tuesday that did not give figures.
The Nigerien probe "revealed serious deficiencies with regard to the arrangements anticipated (by Niger) for maintaining order to manage the situation," it said.
This "caused the French army to turn to the use of force to extricate itself from the pressure of the demonstrators."
"Meanwhile, the investigation carried out by the French army, while acknowledging that the convoy used force to extricate itself from the threatening crowd, concluded that the situation unfolded in line with regulations, using warning shots," it said.
In addition to the three protestors who were killed, 17 civilians, seven Nigerien gendarmes and seven French soldiers were wounded, it said.
The convoy, which had begun its journey in Ivory Coast, took place at a time when France was facing mounting hostility in Mali.
The Nigerien statement said the protest in Tera had been organised.
The demonstration "was far from being a spontaneous event," it said, adding that most of those involved were school pupils.
Bazoum replaced the interior minister and head of the gendarmerie after the incidents.
The poorest country in the world according to the benchmark of the UN's Human Development Index (HDI), the landlocked Sahel state is facing jihadist attacks on two fronts.
Groups linked to Al-Qaeda and the Islamic State have carried out massacres in the west of the country, while jihadists associated with Nigeria's Boko Haram and the Islamic State West Africa Province (ISWAP) have conducted attacks in the southeast.