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Young pace bowler Duffy has a quadriceps strain, and red-hot opening batsman Aaron Redmond has a bulging disc.
''There is also a lot of soreness from some of the other players after the hectic playing schedule we have had this season,'' coach Vaughn Johnson said. He will assess the fitness of the team and decide if Otago needs to bring other players north from Dunedin. The team to play Canterbury will not be named until this morning.
Johnson was disappointed the game against Wellington on Tuesday slipped out of Otago's grasp.
''We were disappointed after scoring 349. It should have been enough,'' Johnson said.
He acknowledged his team did not bowl as well as expected.
''It took us a bit of time to settle on a plan on the park. We went for a dollar each way and it didn't work.''
It has been a successful season for Johnson's Otago team, with a win in the twenty/20 and the runner-up spot in the Plunket Shield.
''That's gone now,'' Johnson said.
''We have to forget about that and regroup for the Ford Trophy.''
Johnson has been handicapped because four of his players are playing for the New Zealand XI in the warm-up game against England in Queenstown.
Still, the coach is confident his team can beat Canterbury.
''We just have to get our thinking a bit clearer and our plans a bit more precise on the park and stick with them,'' he said. Johnson realises his players are getting tired after the long season.
''It's a little bit like a horse that has gone around the track 100 times and starts to get tired. That is exactly what we feel like.
''We haven't got an extended squad. We have introduced some young players to fill the gaps. There is not a lot more we can do. We just have to keep battling on.
''It's about making sure that we get the unit functioning as professionally as we can. Up until now, we have.
''We had an off-day with the bat in the Plunket Shield match on Saturday and with the ball on Tuesday. We have to get out of Wellington and move on.''