The ALS Therapy Alliance objects to a joke in the film where Mark Wahlberg's character argues with another man by saying: "From one man to another, I hope you get Lou Gehrig's disease!"
ALS has long been referred to as Lou Gehrig's disease since the legendary baseball player was diagnosed with the illness in 1939.
Traci Bisson, a spokesperson for the ALS Therapy Alliance, has condemned jokes at the expense of ALS patients in a statement.
"We want to make it clear that ALS, or Lou Gehrig's disease, is not a laughing matter for people and families suffering from this life-threatening illness. The punch line in the movie Ted comes at the expense of people afflicted with ALS," Bisson said.
Bisson went on to clarify that the organisation is not "condemning" MacFarlane, rather thar she hopes this will simply be a learning experience for the writer-director.
"We just want to stop this alarming trend before it becomes too widespread. We work every day with a dedicated community of supporters to raise awareness and funds, aiming to wipe out ALS," Bisson explained.
"We hope the filmmakers move beyond the unfortunate way Lou Gehrig's disease is used in the film and join us in finding a positive way to raise awareness and research funding to help find a cure."
MacFarlane's Ted topped the US box office over the weekend by taking in $54 m.
Ted is now playing in the US and is released on August 1 in the UK.
Watch a trailer for Ted below: