The 23-year-old South-African born player has a stress reaction in a bone in his right foot and it is unlikely he will be fit in time to feature again this summer.
Best-case scenario is he might be available for Otago's last couple of first-class games in late March.
It is blow for Barnes who had a terrible run with injuries last season.
He hoped a shift from Auckland to Otago would bring about a change of fortune and he certainly showed great potential during the twenty20 campaign.
Barnes was the joint leading wicket-taker in the competition with 15 wickets at an average of 19.
He bowled with some good heat and his yorker, in particular, proved a very useful delivery.
But he injured his foot during a trial match before the one-day campaign and was not really able to operate at 100%.
He hobbled through four games, taking six wickets at 28 before he succumbed.
"That's probably how it is looking at the moment,'' Barnes said when asked if he would be out for the remainder of the season.
"I would have liked to have played through all of the one-dayers. That was one of my goals.
"But I'm very pleased [with how the season went], especially compared to last season.''
Barnes was contracted to Auckland but did not get on the park.
He had a groin injury, a back complaint and two different foot issues which kept him sidelined.
Just getting on the field was a triumph but, having tasted success in the twenty20 tournament, Barnes was keen to find out what he was capable of in first-class cricket.
And with Neil Wagner named in the test team yesterday, Barnes' extra pace would have been a blessing for Otago.
"I really did want to play some red-ball cricket.
"Before my injury I talked to Monty [team physio James Montgomery] about maybe playing a couple of four-dayers and that would have been really unbelievable.
"I'm gutted I won't get to play any four-dayers at this stage but there might be a chance I can play in the last one or two games.''
Barnes has been included in New Zealand Cricket's winter training programme at Lincoln, so he is clearly a player who has been identify has having potential to play at a higher level.
"I'm very pleased. I didn't get through the whole season but I must have done something right.''
Barnes has not given any thought as to where he might play his cricket next summer but said he has enjoyed his stint in the deep south.
