But the 31-year-old is expected to regain full fitness ahead of England's one-off encounter with Scotland on June 10 before they face Australia three days later.
England have rested wicketkeeper-batsman Jos Buttler for the match in Edinburgh, with Sam Billings drafted in as replacement in the 13-man squad.
Buttler and pace bowler Tom Curran will return to a 14-man squad for the five-match series against Australia starting on June 13, while Billings drops out.
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Limited-overs specialist Alex Hales and Adil Rashid have been selected in the two squads alongside all-rounder Moeen Ali, who was dropped from England's test side during the tour to New Zealand in March.
England, who are number one in the ODI world rankings, beat hosts Australia 4-1 in a five-match series in January.
Squad v Scotland
Eoin Morgan (captain), Moeen Ali, Jonny Bairstow, Sam Billings, Alex Hales, Liam Plunkett, Adil Rashid, Joe Root, Jason Roy, Ben Stokes, David Willey, Chris Woakes, Mark Wood.
Squad v Australia
Eoin Morgan (captain), Moeen Ali, Jonny Bairstow, Jos Buttler, Tom Curran, Alex Hales, Liam Plunkett, Adil Rashid, Joe Root, Jason Roy, Ben Stokes, David Willey, Chris Woakes, Mark Wood.
(Reporting by Hardik Vyas and Shrivathsa Sridhar in Bengaluru; Editing by Peter Rutherford and Ken Ferris)
