In a series of posts on Twitter, Cain suggested that Adele had been punished by the panel for her commercial success.
"Some of these Mercury nominees are hilariously obscure," he said. "To think they once nominated Spice Girls and early Take That!
"I think judges try to out-cool each other by coming up with increasingly unknown + alternative acts. My votes are for Elbow + Adele!
"PJ Harvey wins Mercury for obscure album no-one liked or bought - how predictable! What's wrong with music connecting with lots of people?"
He added the next morning; "To clarify, I didn't say Polly Harvey is obscure, I said her ALBUM is. Don't think it's her best I'm afraid...
"And 70,000 sales in country of 60m is nothing. I just don't think artist like Adele should be penalised for connecting with mass market.
"But I have nothing against Polly Harvey, I object to Mercury judges + their obsession with cool! They're like indie kids at school who raved about bands until they got in the charts when they'd ditch them for having sold out. So boring!"
Harvey's record has experienced a reported 1,000% increase in sales since last night's victory.
On his Twitter biography, Cain notes that despite his position at Channel 4, all thoughts posted on the social networking site are his own. Cain also sits on Channel 4's Arts Board.
> PJ Harvey's Mercury-winning album 'Let England Shake' - track-by-track
Watch Digital Spy at the Mercury Prize below: