Eyewitnesses said the vehicle belonged to AGHRYMET, which administers hydrology and meteorology programmes related to agriculture and is affiliated with the Permanent Inter-State Committee for Drought Control in the Sahel (CILSS).
The car was burnt near the University of Niamey campus where protesting students have erected barriers of burning tires. No one was injured in the attack and eyewitnesses said police intervened with teargas to disperse the mob.
Last year, a car belonging to CARE International, an aid agency, was covered in petrol and burned in Niamey. Other aid agencies have said the threat of violence against them have prompted some to remove the stickers and identifying marks from their vehicles.
The University of Niger National Students Union has been protesting against the deployment of state security personnel on their campus and the detention of several students. It has not explicitly recommended students to target aid agencies.
Since March, primary and secondary school classes have also been disrupted in Niger by intermittent schoolteacher strikes over pay, prompting school students to rampage in Niamey.
Earlier this month, rioting students near the university "lynched" three soldiers according to the interior ministry.