Plunkett played in the drawn series opener at Lord's before sustaining a left side strain while playing for Durham against West Indies 'A' over the weekend after he'd been allowed to play by England's management in a bid to get some batting practice.
He was selected in a 14-man squad for the second Test at Old Trafford which starts on Thursday but after consultations with physio Kirk Russell early Tuesday he has been ruled out of the next two Tests.
Fast bowler Sajid Mahmood could now be recalled at his Lancashire home ground while Gloucestershire seamer Jon Lewis is also in contention.
Plunkett will have a further scan on the injury and is also rated as a doubt for the final Test at The Oval starting on August 17 but England are hopeful he will be fit enough for the subsequent one-day series against Pakistan.
Already on England's long-term injury list are Ashes-winning captain Michael Vaughan, whose knee problem means he has been ruled out of the Test series in Australia later this year, star all-rounder Andrew Flintoff (ankle), fast bowler Simon Jones (knee) and spinner Ashley Giles (hip).