Hughes died on Thursday, just three days before his 26th birthday, after being struck on the head by a bouncer in a Sheffield Shield match at the SCG on Tuesday. He had emergency brain surgery after the incident.
AFL CEO Gillon McLachlan told AFL.com.au of his shock at the news of Hughes' passing.
"It's one of the worst pieces of news I've ever received," McLachlan said.
"I'd just like to say, on behalf of the industry, all our clubs here – (and) as I guess, a brother sport – we’re thinking of the Hughes family at the moment and cricket and his friends and people in cricket.
"This is going to be a very tough period for all of them and it's a terrible day.
“On behalf of the industry, I just want to acknowledge the fact that we're thinking of them, and acknowledge what a terrible loss he’ll be."
AFL media relations manager Patrick Keane also tweeted: "The AFL extends its deepest sympathies to the family of Phil Hughes, his friends & teammates and sporting colleagues at Cricket Australia."
AFL Players' Association president Luke Ball said in a statement: "We extend our deepest and utmost sympathy to the family and friends of Phillip Hughes. Today's news is utterly shocking and so very sad.
"For someone to be taken so young and with so much life ahead of him, pursuing his dream, is devastating and hard to comprehend.
"As fellow sportsmen, our thoughts are with his teammates, close friends and everyone in the cricket community during this difficult time."
Overcome by sickening chills after hearing of Hughes' passing. A horrible tragedy. Speechless. Thoughts with his family and friends #RIP
— Steve Morris (@stevemorris38) November 27, 2014
Extremely saddened by the news about Phil Hughes . My thoughts are with everyone that he touched , which sounds like a lot of people #rip
— dayne beams (@beama17) November 27, 2014
Such devastating news. Totally shocked. Remind those closest to you how much you love them. Life is so fragile #RIPphilhughes
— Nathan Jones (@nathan2jones) November 27, 2014
Sad to hear of the passing of Phil Hughes at the young age of 25. Thoughts are with his family, friends and team mates. #RIP
— Luke Hodge (@LHodge15) November 27, 2014