Television watchdog Ofcom has received 180 complaints from upset viewers about Monday night's instalment of the ITV soap.
Character Aaron Dingle (Danny Miller) has been suffering homophobic abuse in prison since the other inmates found out he is gay, and he has also been victimised as the son of convicted paedophile Gordon Livesy who hanged himself in the jail in 2016.
Aaron, who was abused by his father as a child, was dragged to an empty cell by an angry mob of prisoners during the episode and beaten by ringleader Jason who spat homophobic insults at him.
He then said: "Your pansy old man died in here."
The character continued: "This is where he laid at night thinking about all the things you and him got up to.
"Did you cry for him to stop, or did you secretly want him to carry on?"
As he held Aaron to the bed, he said: "Then he climbed up on his bed, exactly where you're kneeling now.
"I reckon the last thought that went through his head, your dad, was that it was worth it because he ruined you."
An Ofcom spokesperson said: "We will assess these complaints before deciding whether to investigate, or not."
An ITV spokesperson responded: "The threat of violence towards Aaron Dingle was signposted both before and during last night's episode, which included a pre-transmission warning of scenes some viewers might find upsetting.
"The issue of violence in prisons is a real and highly topical one, and many viewers have praised the storyline for highlighting the homophobia some people face within the criminal justice system.
"The actual violence shown towards Aaron was, however, carefully judged and suitably limited, given the scheduling of the programme."
Viewers of the Yorkshire Dales-set soap were shocked by the scene and tweeted their reaction.
@elizabethmphill wrote: "@emmerdale found last night's just TOO sickening too watch had to switch off."
@DianeBr85967895 wrote: "@emmerdale I have watched Emmerdale since the start. I have now switched off. The storyline at the moment is horrendous."
@ryanlewis79 wrote: "Jeez them scenes from Emmerdale last night were horrendous, watershed much..."
@olivescottwhild wrote: "Honestly at this point idec about watershed. This storyline is unnecessary and harmful for csa and rape survivors. #Emmerdale"
Some fans tweeted Ofcom to complain.
@sarina_kophia wrote: "@Ofcom hi @emmerdale is extremely distressing and totally inappropriate for this time of the evening!"
@welsh_gemz wrote: "@Ofcom don't really think the prison beatings in @emmerdale are suitable for prewatershed."
But other viewers thought it was an important storyline that had been handled well.
@AlisonJayne82 wrote: "Have to say amazing episode. Glad things like this are being shown before the watershed as it does help to educate younger people."
@Probets69 wrote: "Danny Miller is an absolute inspiration to any working actor. Consistently Superb! #Emmerdale #Itv #actor."
In 2016, Emmerdale received 815 complaints in total with 550 of them over a dognapping storyline.