The former Ireland batsman was included in England squads for both the Scotland match and the Australia series announced Wednesday despite suffering a finger injury fielding for county side Middlesex during a One-Day Cup match against Somerset on Sunday.
Morgan will miss the Twenty20 fixture at Lord s after chipping the end of his right ring finger.More news: Roseanne Barr Blasted for Blaming Michelle Obama for Show Getting Pulled
England squad for 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.
England bowler Tymal Mills and Surrey all-rounder Sam Curran have also been added to the World XI squad.More news: Sanchez takes charge in Spain as tarnished Rajoy departs
But while he won't be able to play in that match, Morgan will take charge in Scotland and then in five matches against Australia starting at The Oval on June 13.
Meanwhile, Tymal Mills, the England worldwide, and Sam Curran, the Surrey allrounder, also have been added to the squad, making it a 14-member roster. "It is not a huge concern, it is one we can hopefully manage past in about a week", said Flower, according to official International Cricket Council (ICC) website.
Following that match, England will play a limited overs series against Australia, which will consist of five ODIs and a one-off Twenty20 global. He is the brother of Tom Curran, who made his England debut last summer and has since played for them in all three formats.More news: Waymo signs deal for 62,000 Chrysler Pacifica Hybrids
All proceeds from the Lord's match will be used to redevelop the stadia in the Caribbean, which were damaged due to hurricanes past year.