"There are no words strong enough to express the ignominy of these terrorist acts," a statement from his office said.
Supporters of the president reported that his motorcade was targeted as it moved through the town of Arcahaie north of the capital Port-au-Prince.
The town has been regularly rocked for almost two years by residents demonstrating against a redistricting decision by the former president.
In July 2015 then-president Michel Martelly issued a decreee to split the town into two districts, enraging locals.
The statement condemned the rock-throwing as "acts endangering the life of the President of the Republic."
The Caribbean nation, the poorest country in the Americas, is also grappling with the aftermath of a January 2010 earthquake, with tens of thousands of people still living in tents without proper sanitation.