The 31-year-old sustained a stomach injury while bowling during a warm-up match against Canterbury in Lincoln yesterday.
He got through just four overs before succumbing to injury.
Otago coach Mike Hesson was unsure whether the complaint will rule the bowler out for the opening game.
"He'll see the doctor and we will find out in a couple of days," Hesson said.
In McSkimming's absence, Otago left-armer Craig Smith had to carry a heavy workload.
He bowled 32 overs on the trot and took one for 86.
Neil Wagner bowled well, taking one for 40, and Sam Wells impressed with one for 42.
But part-time spinner Hamish Rutherford was the pick of the bowlers with two for 51 from 16 overs.
In reply to Otago's 365, Canterbury reached 312 for six from 101 overs.
"I was very pleased from a bowling point of view. We bowled well on a flat wicket and the guys bowled with real intent," Hesson said.
"We dropped a couple of catches in the field, which is something we can work on. But overall I was very pleased with the day."
The teams will start from scratch today with Canterbury in the field.
