Despite a police presence, nine buses taking families and vulnerable migrants to a site near Vrasna were forced to turn back as dozens of villagers blocked the road, hurled stones and chanted "close the border" and "throw out illegal migrants," according to images broadcast by public television Ert.
The migrants were finally taken to hotels on the island of Eubee, 400 kilometers to the south.
An IOM statement expressed concern "about the violent incidents that took place in the area of Vrasna," which it termed "an isolated incident."
The IOM urged government and non-government groups "to work together in order to prevent" similar situations from recurring, AFP reported.
Greece has once again become the main point of entry for people seeking asylum in Europe, posing a challenge for the conservative government of Kyriakos Mitsotakis that took over in July.
It wants to create 20,000 places for migrants who are saturating small Greek islands in the Aegean Sea.
Local officials have begun to push back against the government's plans however, with the town of Penteli in the northern outskirts of Athens refusing to take in a group of unaccompanied minors.
People who support the migrants have launched a leaflet campaign, and red paint was splattered on the Penteli town hall early Thursday, Greek media reported.