It is estimated more than four million people were waiting for operations in June - a figure last seen in 2007.
The rise is partly because of growing demand and the NHS performing more procedures.
But some doctors argue the higher numbers reflect growing strain on the health service.
The NHS in England is failing to meet its target to operate on 92% of people within 18 weeks.
Since June last year there has been an increase of more than 21% in the numbers waiting longer than 18 weeks to 373,182.
NHS England said: "Last month 1.4 million patients started consultant-led treatment, and more than nine out of 10 patients were waiting less than 18 weeks.
"We're working hard to cut long waits, and the number of patients waiting over a year for treatment has dropped by nearly 13,000 since March 2011 to being just over 1,500 now."
The confirmed figures shows that 3.83 million people are waiting to have surgery, but missing data means the NHS believes the figure may in fact be "just over four million patients".
Other targets missed include the four-hour target in A&E and urgent referrals for cancer care.
John Appleby, the director of research at the Nuffield trust, said: "These figures show that the NHS continues to be systematically unable to meet its main targets.
"This puts the NHS on the back foot as we approach winter, with problems both at the 'front door' of A&E departments and at the 'back door', as hospitals struggle to send people home or onto further care."
The number of people waiting for routine surgery in England is at its highest level for a decade, figures from NHS England show.