Cox launched into a foul-mouthed rant during a show in North Carolina on Friday (04Dec15), when he recalled having a nasty run-in with Corgan while supporting the Smashing Pumpkins on tour.
He claimed the incident was sparked after taking a bottle of water backstage, which allegedly prompted the veteran rocker's bodyguard to approach him and say, "What the f**k do you think you're doing? This is Mr. Corgan's water."
The singer told fans the bouncer then shoved him against a wall, and the following day, Corgan reportedly blasted Cox in person and dismissed Deerhunter as a "s**tty little insignificant f**king indie rock band".
Cox's comments, which were caught on camera and posted online, prompted the Smashing Pumpkins' manager to vehemently deny the allegations and threaten legal action.
"Several eyewitnesses can attest that Cox's account is a complete fabrication, probably to get some much-needed attention," reads a statement issued to Pitchfork.com. "Since this is intentionally slanderous, I will likely suggest we pursue charges unless a retraction is forthcoming."
The stern words have since motivated Cox to backtrack and apologise.
"What I did was open my big f**king mouth and go off on one of my usual tangents," the star confesses. "Some people call this 'stage banter'.
"I do not need, or seek, any attention and in fact was embarrassed that this ended up being uploaded to YouTube, and then considered a news story. I will be the first to admit that there are two sides to every story and it is unfair that I gave mine without the other party being there to counter."
Cox also admits to reading Corgan's "very moving and heartfelt tribute to his deceased friend", former Stone Temple Pilots rocker Scott Weiland, following his tragic death on Thursday (03Dec15) and concluded he doesn't find any humour in "kicking someone while they are down".
Corgan has yet to comment on the controversy.