Harmison has been replaced in England's 13-man squad by Hampshire pace bowler Chris Tremlett.
Durham quick Harmison will see a specialist on Tuesday to determine whether surgery is required.
England's chairman of selectors, David Graveney, said Monday: "We have taken the precaution of adding Chris Tremlett to the squad following confirmation this morning that Stephen Harmison will not be available.
"Chris performed well in the recent England Lions tour match against India and his inclusion will give us additional options when we come to decide on our starting eleven for Thursday."
Harmison aggravated his injury while playing Friday for Durham against county champions Sussex at Horsham where he bowled just five overs before withdrawing from the match.
The 28-year-old was then rated "extremely doubtful" for the first of a three-Test series against India.
Harmison originally sustained the injury at his Riverside home ground nearly a month ago during England's fourth Test win against the West Indies.
However, he opted against immediate surgery after being advised he could play in the India series.
In his absence, and that of all-rounder Andrew Flintoff, still sidelined with an ankle problem, it looked as if England faced a straight choice between Stuart Broad - like Tremlett uncapped at Test level - and James Anderson were for the final place in their side.
The 6ft 7in tall Tremlett, known for his pace bounce, is the son of Tim, the former Hampshire seamer and now he county's director of cricket and the grandson of Maurice, who captained Somerset and also played for England in the 1940s.
He has long been spoken of as a future Test bowler and has played six one-day internationals, the last against New Zealand in Perth in January.
But the 25-year-old has seen his career hampered by injuries with a hamstring problem ruling him out of England's tour of Pakistan in 2005.
Playing alongside Broad for the Lions, England's A side, against India in the drawn three-day match concluded at Chelmsford on Sunday, Tremlett took one wicket for 40 runs in 13
Andrew Strauss (Middlesex), Alastair Cook (Essex), Michael Vaughan (Yorkshire, capt), Kevin Pietersen (Hampshire), Paul Collingwood (Durham), Ian Bell (Warwickshire), Matthew Prior (Sussex, wk), Ryan Sidebottom (Nottinghamshire), Matthew Hoggard (Yorkshire), Monty Panesar (Northamptonshire), James Anderson (Lancashire), Stuart Broad (Leicestershire) and Chris Tremlett (Hampshire).