The plot sees Aaron Livesy (Danny Miller) help to end Jackson Walsh's life, but spinal injuries charity Aspire has warned that it could cause a "great deal of hurt".
Director of Services Alex Rankin told the Daily Star Sunday: "The storyline has been negative, unrealistic and pretty inaccurate. I've watched it very closely and have been incredibly disappointed with how Emmerdale have portrayed Jackson's situation.
"People with spinal injuries are not ill, they do not need to spend all their time in bed being spoon-fed soup. Emmerdale had a great opportunity to be inspirational with this storyline, to show that people who suffer similar injuries to Jackson's can, after much adjustment, go on to live a fulfilling life.
"What worries me is that it's basically saying that life with a spinal injury is not worth living. I don't think they've considered how those people in Jackson's situation will feel when they watch it. I think it's going to cause a lot of people a great deal of hurt."
An Emmerdale spokesman insisted that the story will be told "with integrity", adding: "We approached Aspire, keen to inform them about this storyline, and we welcomed their feedback which was fully taken on board."
Actor Marc Silcock recently described his character Jackson's departure as "an exit people will remember".