The Irish Football Association are to investigate the incident which occurred after North Ireland lost 2-1 in Reykjavik with Gillespie netting the winner ion his own net.
The players were taking their seats on the flight which was heading to London Heathrow at 7:40am Thursday morning when a dispute between the two players occurred.
Other players intervened to stop the situation from getting worse whilst cabin crew staff reported the incident to Ireland manager Nigel Worthington before the flight took off.
A statement on the Irish Football Association website read: "An incident occurred today between team members of the senior Northern Ireland squad which the president (Raymond Kennedy) and chief executive (Howard Wells) are aware of.
"Both the president and the chief executive will investigate the situation and take appropriate action."
Northern Ireland went down to a 2-1 defeat in their Euro 2008 qualifier on Wednesday night.