It is the latest setback to befall Ireland's World Cup campaign after a disastrous warm-up series and uncertain opener against the USA last weekend which has led to a barrage of criticism and pessimistic predictions about Ireland's campaign.
However, fit-again full-back Rob Kearney yesterday hit out at the negative attitudes and called on the nation to get behind the team.
"Our performances in August weren't good enough and the World Cup opening match wasn't good enough," said Kearney. "But I would be more of the nature of getting behind the team at the start and if we do screw up and have a bad tournament, then jump in and give us everything we deserve.
"I think about how everything is going at home, outside of sport, we always look at negatives far more so than we do at positives. It's quite an Irish thing.
"We are really close to clicking. Our intention is to get out of the group, we are one from one and nothing has changed," he added.
Ireland captain Brian O'Driscoll said the team feel a responsibility to do themselves and the country proud this weekend.
"We are the guys that Declan has picked and given the jersey to and we have to give that jersey the respect it deserves and up our performance," said O'Driscoll
Varley will be hoping to get the chance to do just that after his late call-up yesterday. The Munster hooker, who was in the extended Irish squad until the 30 players for the World Cup was announced, said that he was very disappointed for Flannery.
"Obviously, my heart goes out to Jerry. You wouldn't wish injury on anyone. But it is the nature of the sport. One man's loss is another man's gain. I certainly wish Jerry a speedy recovery," said Varley yesterday.
Ironically, he spoke at a Munster press briefing in Cork on Tuesday about the way he had to deal with the disappointment of not making the World Cup squad.
All of that changed yesterday morning when Varley, who was preparing for the PRO12 clash with Scarlets on Saturday, saw Declan Kidney's number appear on his phone.
"When I read the report that Jerry got injured and saw Declan's name pop up on my phone, I got very excited. I've been on a bit of a high since.
"A lot of things were going on in my mind, trying to get organised and stuff. It's lousy on Jerry to get injured, especially at this stage in his career, but y'know I think it's a brilliant opportunity for myself personally and I'm going to grab it with both hands," he enthused.
Varley, whose two caps to date were off the bench against Australia and Argentina last year, expects to be in New Zealand by Saturday following the dramatic turnaround in fortunes.
"In terms of practicalities, I'm cleared by our medical and fitness guys so I'm heading up to Dublin in the morning and flying from Dublin Airport on Thursday evening," said the Limerick man. "I call into IRFU to pick up gear and various things. I don't know what route I'll be taking yet, but I hope to arrive in New Zealand on Saturday."