Questions over the future of the tournament have been raised after seats were ripped up and flares hurled on to the pitch as football fans from the Republic went on the rampage during Monday evening's match against Linfield.
A section of Shamrock Rovers supporters from Dublin clashed with riot police who had been called in to keep rival factions apart midway through the first half of the match, which was broadcast live on television.
It was the latest controversy to hit the competition which has been dogged by sectarian clashes between fans since its inception in 2005.
Setanta Sports has already said it will not be renewing its sponsorship for the competition, leaving its future hanging in the balance.
It was launched after a 25-year gap in cross-border competition, following the scrapping of the Tyler Cup due to the Troubles.
Yesterday, the chair of the cup's organising committee was adamant it still has a future.
"When you look at the overall picture, we've had very little trouble at games," said Milo Corcoran, a former president of the Football Association of Ireland.
"Obviously, I don't condone the hassle we had last night, it was very bad behaviour and it gives the game a bad name, but it was only a small, small few of the supporters that caused the trouble.
"The relationships between all the clubs are excellent."
Shamrock Rovers said it is investigating the violent incidents.
It is believed the club will be handed the repair bill for the damage caused at Windsor Park.
"The club is very disappointed by the behaviour of some of our fans at Windsor Park," a spokeswoman for Rovers said. "We brought over 500 supporters to Belfast. The majority of them got behind the team and enjoyed watching the club progress to the semi-finals of the competition.
"Out of the over 500 fans, about 20 caused the problems that occurred last night; we will take whatever action is necessary."
Sports Minister Caral Ni Chuilin described the trouble as "disgraceful".
The Irish FA – football's governing body in Northern Ireland – said any sanctions against clubs or supporters would be taken by the Setanta Sports Cup committee.
"The Irish FA are aware of the actions of some fans during the Setanta Sports Cup game between Shamrock Rovers and Linfield and unreservedly condemn such acts of inappropriate behaviour in football. We will continue to work hard to promote our Football For All message and the actions of some supporters will not deter us in continuing this campaign," a spokesman said.
A spokesman for Linfield FC was unavailable for comment yesterday, but it is understood members met last night to discuss Monday's disorder.
It came one week after trouble at the first leg of the quarter-final tie in Dublin when two fans were arrested. During that game, a Union flag was erected on a pole inside Rovers' stadium.
• The competition was launched in 2005.
• The inaugural winners were Linfield.
• Crusaders are the current holders, having defeated Derry City in last season's final.
• There were 12 teams in this year's competition, six from each side of the border.
• The prize money for this year's winner is £44,000.
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