The helicopter was traveling in an escort with two other helicopters when it was forced to make a heavy emergency landing. The accident happened near the town of Jolfa on the border with Azerbaijan.
Rescue workers are on their way but there are no reports of any injuries.
Many details about what happened are still unclear, but several ministers are said to have been in the helicopters.
Raisi was on his way home from Azerbaijan where he participated in the inauguration of a dam on the river Aras that was established jointly by the two countries.