Wells had to be replaced by Mark Yeates just before the half hour mark due to a tight hamstring in his left leg.
While it isn't know as of yet exactly how bad the injury is, Wells has to be listed as extremely doubtful for Wednesday's trip to Meadow Lane given the fact that the game is only days away.
The recalled Ricky Ravenhill, who was handed his first league start of the season against Swindon, also went off during the game after taking a whack but he appears to have a greater chance of making the County game.
Parkinson said: "Nahki's hamstring has tighten up, which is obviously a blow for us.
"If you take the top scorer out of any team, it is going to affect them. His presence might have been the difference for us today (Sunday) had he not gone off.
"He has that cutting edge - he is our quality player in and around the box - and the game was crying out for someone like him to be around.
"We're just having a period at the moment where we are struggling to get (James) Hanson and Nahki out on the pitch together. I think most people will agree that those two form probably one of the best strike partnerships in the division but we can't seem to get them on the pitch together at the moment.
"It is clearly a blow that Nahki is out but hopefully it is not too serious."
Parkinson added: "For me, I felt Ricky was our best player.
"He was excellent today - he tackled, chased and passing it well. Unfortunately he took a whack on the knee and we took him off to protect that.
"Before going off though, he definitely added something to the team and he set the tone for us, especially with the first half performance."