Prior withdrew from England duty last month in a bid to get back to full fitness as he battled Achilles, quad and hand injuries.
The 32-year-old's position in England team had already come under considerable scrutiny after below-par performances with both gloves and bat in the Test series against India.
After he pulled out, Prior's place for the final three Tests went to Jos Buttler and he will remain out of the national set-up for the foreseeable future as he recovers from the operation.
"My Achilles has been the main issue, it's been pretty bad, to be honest.
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"It's not the end, but there is a long road back and it starts from September 4 with four months of rehab to get as fit as I possibly can.
"It was a massive decision, but I went as long as I could. It's been shown by specialists that I couldn't physically have gone on any longer. So it's now time to get it right, get fit again and come back stronger."