Meanwhile CA also said left-arm fast medium bowler Mitchell Starc was returning home with "some lower back soreness".
Australia coach and selector Darren Lehmann said dynamic batsman Warner had been left out of the one-dayers, which start with a lone ODI against Scotland in Edinburgh on Tuesday before a five-match series with England begins in Leeds on Friday, because of a lack of runs at this level.
"David has been left out of the Australian ODI squad for this tour purely due to his recent lack of form in this format," Lehmann said in the CA statement.
Warner played in just one match during Australia's involvement in the Champions Trophy in England in June, scoring nine in a loss to England, but was suspended from the team after punching England's Joe Root in a Birmingham bar after the match.
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He has only played three more ODIs this year, in January against Sri Lanka, where he scored 10, 60 and four.
"Like all selection matters, it was a tough decision, but like all players he understands the situation and knows he needs to get back to playing RYOBI Cup (Australia's domestic one-day competition) and making a heap of runs that we can't ignore," Lehmann added.