The 25-year-old, who is pressing for a Test recall, crashed to the ground unconscious after the heavy blow to the lower head and was rushed to hospital from the Sydney Cricket Ground.
Television images showed the helmeted Hughes, who had scored a composed 63 for South Australia in the Sheffield Shield game, standing dazed before going down face-first following the rising delivery from New South Wales bowler Sean Abbott.
New South Wales players, including Test colleagues David Warner and Brad Haddin, quickly rushed to his side and immediately called for help.
"They've finished the surgeries but he's still in a critical condition," said David Faktor, a spokesman for St Vincent's Hospital, where Hughes was taken. "Now they'll just monitor him."
Reports said he was in an induced coma in the intensive care unit and being treated to relieve pressure on his brain from bleeding.
Tim Nielsen from South Australia Cricket read out a statement from the Hughes family outside the hospital.
"The outcome of the surgery is unlikely to be known for the next 24-48 hours," he said. "We would appreciate it if you would look after the family and friends and respect their privacy please."
Cricket Australia (CA) said in a live match blog on its website that Hughes had "been leaving the short balls, had a go at this one, misjudged it and was hit in the head. He blacked out and fell badly". The match was abandoned.
Medical staff worked on Hughes, including mouth-to-mouth resuscitation and oxygen, for more than 30 minutes before he was taken from the field.
The accident, with Hughes' mother and sister in the stands watching, sparked an outpouring of support for a player who is well-liked and respected in cricketing circles.
"Our thoughts and prayers are with Phil Hughes right now. We are also thinking of his family, team-mates and friends in the Australian cricket family," said CA chief James Sutherland, adding that the news "sent shudders" through him.
National coach Darren Lehmann tweeted, "Our thoughts and prayers are with Phil and his family. He is a great fighter and great young man."
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It's very tragic he passed away. Sad day for cricket.
All the prayers for this young batsmen. Get well soon dear!