The ECB said on their website that the Durham player, who will miss most of the domestic county season, has undergone scans and seen a spinal specialist this week.
"The scans confirmed an ongoing bone stress reaction in his back and Onions has been advised that he will need to undergo a further period of rest and rehabilitation programme of up to 12 weeks in duration," it said.
"Onions also underwent surgery yesterday at a London [ Images ] hospital to repair cartilage in the front of his left knee and the rehabilitation period required will be of a similar length to that prescribed for his injured back."
Onions, who has not played for England since January and was ruled out of a two-Test series against Bangladesh in March due to the back injury, said being fit for the Ashes tour to Australia [ Images ] later in the year is his priority.
"I am naturally incredibly disappointed to miss the bulk of the domestic season and am still hopeful that with rest I can be back on the field nearer to the end of the summer," he said.
"The ECB medical team has been very supportive and all I can do is be patient, work hard on my rehabilitation programme and focus on my number one goal, which is to be fully fit and available for selection for the Ashes tour to Australia."