Duffy will be out for next six weeks after fracturing a metatarsal in the latter stages of their 3-0 defeat at Nottingham Forest on Saturday - Brighton’s second consecutive defeat which threatens to derail their promotion push.
It also means Ireland must plan without the Derry centre-back when they face Wales in their World Cup Group D qualifier at Aviva Stadium on March 24.
Duffy was a starter in the impressive 1-0 win over Austria in Vienna in November, and was likely to be in O’Neill’s first XI again.
Duffy will also miss the friendly international with Iceland the week after the game against Wales.
“Thanks for all your messages, op in the morning to get it sorted! Will be back stronger for big push to end off the season,” Duffy posted on Twitter yesterday.
Duffy has made 31 appearances since joining the Seagulls from Blackburn in August.
Brighton manager - and former Ireland assistant boss - Chris Hughton said yesterday: “He’s fractured his fifth metatarsal and will have an operation probably tomorrow.
“He’s probably looking at a minimum of six weeks. It’s a big loss, particularly at his stage of the season, and also more for him because he’s had a wonderful season so far.”
After two defeats on the spin, Brighton will travel to Rotherham tonight desperate for a win as they continue their promotion chase.
Meanwhile Northern Ireland boss Michael O’Neill admits he would be “tempted” if Premier League side Leicester wanted him to become Claudio Ranieri’s successor.
The Foxes hierarchy will this week meet with caretaker boss Craig Shakespeare to discuss his prospects for the role and the case for Ranieri’s former number two has been strengthened by back-to-back victories.
Others have been sounded out about the vacancy, though, and both former England boss Roy Hodgson and current Northern Ireland chief O’Neill have reportedly been on the club’s wishlist.
O’Neill guided his country to the knockout stages at Euro 2016 last summer, their first major tournament finals in three decades, and are well placed to attain a play-off berth for World Cup qualification in 2018.
The 47-year-old has three years remaining on a deal that includes a £750,000 release clause but admits the lure of Leicester would intrigue him were they to come calling.
“I think you’re always tempted - you have to consider these things if the opportunity is presented to you,” O’Neill told BBC Sport at the unveiling of a new education and heritage centre at Belfast’s Windsor Park.
“I have a good relationship with the board and the (Irish Football) Association here. I’ve been in the job five years now and I’m contracted for another three.
“I don’t think you can ever say ‘no’ in football. Equally I’m not actively looking for another job; I’ve said that all along.
“When vacancies have arisen, particularly in England this year, my name has been mentioned but I actively haven’t sought to find another job outside the one I’m in.”