South Australia's Hughes was felled by a Sean Abbott delivery on day one of their Sheffield Shield clash with New South Wales at the SCG.
The left-hander, who stood dazed before falling after being hit, was rushed to hospital.
A St Vincent's Hospital spokesperson confirmed Hughes was in a "critical condition" after sustaining a head injury.
South Australian Cricket Association high performance manager Tim Nielsen said results of the surgery were unlikely to be known for 24-48 hours.
Cricket Australia chief executive James Sutherland said Hughes' health was the priority.
"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," he said in a statement.
"His welfare is our highest priority. We're also naturally concerned about all of those involved in today's game and will be giving them our utmost support."
Australian Cricketers' Association chief Alastair Nicholson sent his best wishes.
"We were obviously shocked to learn of the seriousness of the incident involving Phil," he said.
"While we have faith that he's receiving the best available treatment, the situation will impact his family, friends, and those directly involved on the field.
"The ACA is therefore working closely with CA to arrange the appropriate counselling for those affected. Naturally our thoughts are with him and we wish him well from all the ACA members."
Hughes was considered a leading candidate to replace injured captain Michael Clarke for the first Test against India starting in Brisbane on December 4.
Several members of the cricket community sent their well wishes on Twitter, including Australia coach Darren Lehmann.
"Our thoughts and prayers are with Phil and his family! He is a great fighter and a great young man!" Lehmann tweeted.