The singer made the comments in response to Ed Droste of Brooklyn-based indie-rock group Grizzly Bear, who was expressing his disappointment at being snubbed in this year's nominations.
"This is why i hate the grammies. because it allows you to question what you've done. don't question what you've done Ed [sic]," Vernon tweeted.
He continued: "Y'alls music is pure as f**k and there is nobody making music like you and I think it's truly unique. The grammies aren't a measure of much that is calculable or quantifiable by our own contexts for music. Why you create is most important."
Droste had said that the Grammys are "literally based off sales" and joked he was "super relieved Taylor Swift is up for another award" because he "was worried she didn't have enough". He has since insisted that his comments were "tongue in cheek".
Vernon previously said he was uncomfortable accepting 'Best New Artist' at the 54th Grammy Awards and called the ceremony "too self-important".
The 55th annual Grammy Awards will be held at LA's Staples Centre on February 10, 2013, with Frank Ocean and fun. leading the nominations.
Watch Bon Iver's 'Holocene' video below: