With first-choice keeper-batsman Jos Buttler and all-rounder Ben Stokes due to arrive back from the Indian Premier League, Morgan believes England would not be able to field another specialist batsman in their final 11.
"It is looking like that at the moment, which is unfortunate for him (Bairstow)," Morgan told British media. "You can't guarantee how often he would be used.
"We've a really strong batting lineup, particularly when Stokes, Chris Woakes and Buttler come back in. I'm not sure about justifying an out-and-out batter at seven.
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All-rounder Moeen Ali offers another off-spinning option in England's 15-man squad and Morgan is keen to use him ahead of Bairstow to bring more stability to the hosts who will start their campaign on June 1 against Bangladesh at The Oval.
"With Ben coming back into the side, it allows us to play another all-rounder - with Mo at seven," he added. "I suppose you could go five out-and-out quicks, with Ben and one spinner.
"But planning towards the tournament, we envisage better weather and slower pitches so we'll need slower bowlers potentially."
Bairstow scored a career-best 174 for Yorkshire against Durham last week in the One-Day Cup to add to his already impressive numbers in the test format, with 1,470 runs at an average of 58 last year - the most ever by a wicketkeeper.
(Reporting by Hardik Vyas in Bengaluru; Editing by Ken Ferris)
