Regular full-back Colin O'Sullivan broke his ankle a week ago and is out of action for the rest of the season, while outstanding forward Rory Keating was injured playing with his club at the weekend and is also ruled out.
According to team official Lorcan Murphy the twin loss is a big blow as they chase their fourth title in a row: "The injuries couldn't have come at a worse time", he said. "I would have been happy enough going into the game with both players, but now it's a different story.
"Coláiste Choilm must win to stay in the title race and we cannot afford to be beaten by more than four points, otherwise we could go out. It's going to be very difficult for us and I'm hoping the lads can lift it for one more big game."
Ballincollig have the potential to win, but will have to improve greatly on the form displayed against St. Brendan's last time out. They rely heavily on full-forward Daniel Goulding for scores, and if he is contained, they'll be in trouble.
Christopher O'Driscoll and Gearóid O'Sullivan should ensure at least an even break at midfield for the champions, and with Paul O'Connor in top form in attack he scored 10 of his side's 14 points against St Brendan's last time out Coláiste Na Sceilge should take at least a point which would guarantee them a place in the knock-out stages.
Another big game in football tomorrow is the all-Kerry clash of Intermediate School Killorglin and Tralee CBS at Fitzgerald Stadium, Killarney.
The Green are in real danger of going out of the championship as they face a highly talented ISK side who crushed Dingle CBS in their previous outing by 13 points. Dingle had earlier beaten Tralee comfortably (1-10 to 0-4) in round one.
Darren O'Sullivan, James O'Reilly, Ray O'Connor, Eoin O'Mahony and Michael Hallissey are ISK's key players and, despite the best efforts of Enna Ó Flatharta, Cathal Ó Súilleabháin, Jason Ó Murchú and Donal Ó Riain, should secure the victory to put them into the last eight.
South Limerick Schools have caused a bit of a stir in only their first season playing in Corn Uí Mhuirí. They won the local derby game with Limerick City Schools and if they take a point from St Flannan's in Cratloe tomorrow they will qualify for the knock-out stages.
Stephen Garvey, Jimmy Barry-Murphy, James Ryan and Maurice O'Connell will again spearhead the Limerick challenge, which should be good enough to ensure they stay in the title race after Christmas.
The Irish Examiner Harty Cup is also hotting up, with three of the four games down for decision tomorrow vital for the participating teams.
Shannon Schools have no injury worries for their tie with Waterford Colleges at New Inn. According to team official Alan Cunningham, the Clare side are thrilled to be involved and will be going all out for the win, which would put them well in line for a place in the knock out stages.
"The round robin system has been very beneficial to us. This will be our third outing tomorrow and with a full squad to pick from, we'll give it our best shot".
Waterford Colleges are in a similar situation with full points from two games. They surprised fellow Waterford team DLS in their previous outing, and if Mark O'Gorman, John Kindregan, John Morrissey and Patrick Hurley are in form, the Clare side, despite the best efforts of David Barrett, David Reidy, Cathal King and Damien Browne, may have to settle for second best.
Midleton CBS and Douglas CS, who clash at Kilbarry (Delany's pitch) tomorrow, need to win to stay in the title race. Midleton are unbeaten after two games while Douglas lost one of two.
With most of their players deeply involved in club activity, it may take its toll on the Douglas side who are already through to the concluding stages of the football championship.
In the same section, the clash of table toppers Doon CBS and Our Ladys at Cashel is another vital tie and the Templemore school cannot afford another loss while a win would put Doon into the last eight.
St Brendan's will look to salvage something from the season when their under-15 footballers play St Flannans in the Moran Cup final at Glin on Thursday (1.30pm).
The Killarney school have won two of the last three finals and, having shown excellent form in earlier rounds, will be favourites to regain the title.
* All the Harty Cup and Corn Uí Mhuirí games have a 2pm start.