Initial reports on Monday suggested he would only miss the first Test starting at Lord's on Thursday in which his place in England's 13-man squad was filled by Hampshire pace bowler Chris Tremlett.
Confirmation that Durham quick Harmison would miss the three Test series came after it emerged that he required surgery which was due to take place later Tuesday.
The operation is expected to sideline him for four to six weeks.
Coach Peter Moores confirmed: "He's going to have the operation later today.
"Unfortunately for him the hernia has come back and now it's all about getting it done as quickly as possible."
Harmison first sustained the injury during the final Test against West Indies at Chester-le-Street nearly a month ago but after tests England's medical staff agreed to let Harmison play on.
But he suffered a recurrence of the problem during Durham's championship match against Sussex at Hove last week and is now set to miss the remainder of England's summer.
Harmison retired from one-day international cricket last winter so his next international commitment is likely to be England's Test tour to Sri Lanka in December.