"Dozens of people were hurt, mainly suffering respiratory problems, and three had to be taken to hospital," MSF official Achileas Tzemos told AFP of the incident near the Idomeni crossing, a frequent flashpoint.
A Macedonian police source said three officers were also injured by stones thrown by the protesting migrants.
Tzemos also said several of the migrants were injured by plastic bullets but Macedonian police denied using such ammunition.
"We are not using any kind of bullets as they are in Macedonia forbidden by law. We are not using batons as we are on the other side of the fence," she said.