"We have no official report at hand at this time but there is no place in the game of football for such behaviour that I am led to believe happened on Saturday," IFA president Kennedy told BBC's Good Morning Ulster on Monday.
"(But) The referee's report should be at hand today and we will set up the investigation and the procedures that have to be followed immediately (once we get the report)."
Speaking on Saturday evening, Kennedy acknowledged that expulsion from the competition was "a real possibility" for both clubs.
A spokesman for Larne said that the club had already set up its own investigation into the incidents.
The Larne official said that the possibility of the club imposing its own bans on players "isn't being ruled out".
"That kind of thing has no place in local football or any football for that matter," said the Larne spokesman.
"Whatever steps are necessary, we will take them - including the banning of players or the fining of players. We are ruling nothing out."
Newry chairman Paul McKenna said he expected his club's players to be "exonerated and to be in the next round of the Irish Cup".
Cullen Feeney could have been very seriously injured with the boots being aimed at his head
Newry City chairman Paul McKenna
"Anybody who reads the papers or what was at the game would see that the Newry players, stewards, fans and management team conducted themselves professionally," added the Newry chairman.
"Our players when the issue broke out did their best to defend themselves.
"I am thankful that nobody was seriously injured. We have a number of injuries to players but none of them are life-threatening.
"Cullen Feeney could have been very seriously injured with the boots being aimed at his head."
Match referee Crangle said that he was left with no option but to abandon the cup tie.
"There were melees developing all over the pitch involving players and substitutes and coaching staff from both dug-outs - I was left with no alternative," said the referee.
"In all my time in refereeing, I have never seen anything so farcical."
Liam Hogan was sent-off for raising his hands to Newry player Darren King and then Alan Reid was dismissed for a challenge on King soon after.
Larne boss Millar was sent from the dugout and then substitutes, players and coaching staff from both sides became embroiled in trading punches and kicks all over the pitch.
BBC Radio Ulster pundit Alan Paterson described the trouble as "the worst scenes I have ever seen in 40 years of watching Irish League football".
Newry boss John McDonnell said the unsavoury events had "kicked off out of nothing".
"It is was not nice what happened - I tried to get my players off the pitch as quickly as possible," said McDonnell.
"We were cruising with seven or eight minutes to go and I'd like to be talking about a cup win but instead we have to wait on the referee's report."
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