Gyan was replaced in the 51st minute after he picked up a groin injury.
The Ghana international is now facing a spell on the sidelines after the latest setback.
The 32-year-old has taken the India top-flight by storm,impressing heavily in the league.
However, the side will have to do without their talisman for the next couple of weeks.
NorthEast are top of the ISL with eighth points from four games, and will next host Mumbai City FC at the Indira Gandhi Athletic Stadium on November 27.