McSkimming injured his back while taking a catch in the drawn match with Central Districts in Invercargill last week.
"He landed on his back and it just hasn't come right yet," Otago coach Mike Hesson said.
"We're hopeful he will be all right for the next game but we'll just have to wait and see.
"He's been for a scan and we haven't had the results back yet."
It is a big loss for Otago.
McSkimming has been one of the linchpins for the past four or five seasons and is the team's leading wicket-taker this summer with 20 first-class scalps at an average of 26.95.
His ability to plug away at an annoying line and length will be sorely missed.
Strapping pace bowler Mathew Harvie will replace McSkimming in the twelve, and top-order batsman Leighton Morgan comes into the squad for Neil Broom, who is on national duty.
Harvie, Anthony Bullick and James McMillan will compete for spots with Neil Wagner spearheading an attack which is still without the injured Ian Butler.
One is destined to carry the drinks.
Harvie has been struggling with a back injury but is fit and should get the nod.
Bullick is a much-improved player and bowled well against Wellington earlier in the campaign, taking three for 53.
McMillan is the quickest of the Volts' bowlers but has slipped down the pecking order in the past two seasons and will be looking to finish the season well.
Morgan has been solid rather than impressive with 272 runs at 30.22, but he earned the team's respect when he got out of his sick bed to post an undefeated 71 the last time these two sides met.
Auckland keeper Gareth Hopkins returns from national duty and will resume the captaincy from Richard Jones.
Anaru Kitchen makes way for Hopkins in an otherwise unchanged squad from the side that dispatched Wellington by 10 wickets in the last round.
The comprehensive win over Wellington still leaves Auckland at the foot of the competition table but coach Paul Strang was pleased with his side's efforts, especially with how his bowlers responded.
"It was a great result for us, especially given the game was even in the middle of day three," he said in a press release.
"In the end we got about as much as we possibly could out of the game: the batsmen got runs and time in the middle, and the bowlers got a good work-out and wickets to boot."
Otago is in third place with 18 points from six matches.
Northern Districts leads with 28 points from Canterbury on 20.
"It's a pretty tight competition," Hesson said, adding the Volts were still ruing poor weather which denied them an opportunity to push for an outright victory in Invercargill last week.
"You can't do anything about that but I was really pleased with the way we played the majority of the game.
"It was probably one of the best bowling and fielding efforts from an Otago side in some time."
Aaron Redmond made a brilliant return to the four-day game with a century.
The classy top-order player has had a frustrating summer watching from the sidelines with a muscle strain.
"He played superbly but it certainly wasn't a swashbuckling innings.
"He is just in a really good head space and making really good decisions.
"He batted for five and a-half hours in Invercargill and looked composed."
The teams at the University Oval, today
Otago: Craig Cumming (C), Aaron Redmond, Shaun Haig, Leighton Morgan, Greg Todd, Sam Wells, Derek de Boorder, Neil Wagner, Anthony Bullick, Nick Beard, James McMillan, Mathew Harvie.
Auckland: Gareth Hopkins (C), Jeet Raval, Tim McIntosh, Richard Jones, Reece Young, Andrew de Boorder, Colin de Grandhomme, Jimmy Neesham, Tarun Nethula, Gareth Shaw, Lance Shaw, Michael Bates.
