Malik was omitted from the ongoing first Test at Lord's with an elbow injury, which Pakistan had hoped an operation two months ago would cure.
But Woolmer, after the second day of the series here Friday, told reporters: "Shoaib Malik is doubtful for the whole series. His injury is not reacting to injections and he might not make it for the Tests."
Malik, 24, has scored 798 runs in 15 Tests at 39.90 with one century, 148 against Sri Lanka, in his last Test appearance at Colombo in May.
He can also bowl off-spin but he has twice been reported for an illegal action, most recently in November.
Pakistan are currently without spearhead fast bowler Shoaib Akhtar, who was omitted from the original tour party with an ankle injury.
Fellow paceman Rana Naved-ul-Hasan then had to withdraw from the tour before the four-Test series got underway with a groin problem
Meanwhile vice-captain and senior batsman Younis Khan (knee) and fast bowler Mohammad Asif (elbow) were both missing from the Pakistan team at Lord's.
In their absence the tourists were 66 for three at stumps Friday in reply to England's first innings 528 for nine declared, a deficit of 462.
But former England batsman Woolmer was optimistic that Pakistan's injury crisis would have improved by the time the second Test started at Old Trafford on July 27.
"Younis Khan and Mohammad Asif are making good progress and we hope to have them available for the second Test," he said.