"Jonathan has been struggling with this condition for quite a while," added Flower. "We have been on tour for about a month and he has had his ups and downs through that month and it is not directly related to that.
"I would also say players commenting to fellow professionals in the media is disrespectful and I think on this occasion he [Warner] has got that horribly wrong."
England's performance squad, which provides back-up to the main party, is also in Australia, but no immediate replacement for Trott has been called into Cook's squad.
Ian Bell could move up the order to number three, while the spare middle-order spot will be filled by Jonny Bairstow, the uncapped Gary Ballance, or all-rounder Ben Stokes, who would offer an extra bowling option.
Angus Porter, head of the Professional Cricketers' Association, said Trott's decision to end his tour was a "brave" one and that his organisation was ready to offer any help to the Warwickshire man.
He added: "It would have been much easier in many ways to plough on, and not address the problem, and maybe that's what people would have done 10 or 20 years ago and we'd never have known why they performed badly.
Jonathan Trott factfile
Born in Cape Town, South Africa, before qualifying to play for England in 2006
Made his Warwickshire debut in 2003 and scored 134
Made his England Test debut against Australia in August 2009 and his 119 in the second innings helped earn a win
"At least we've grown up to the point that people acknowledge it, just as you shouldn't play on with a knee injury you shouldn't play on with a brain injury - you should seek treatment and get yourself right for the future."
Trott made his England debut in the decisive fifth Test of the 2009 Ashes series and his century helped England secure a victory which regained them the urn.
Since then, he has been a permanent fixture in England's Test and one-day teams - scoring 3763 Test runs at an average of 46.45 and almost 3,000 one-day international runs at 51.25.
He is ranked number eight in the world rankings for ODI batsmen and is in the top 15 in the five-day format.
However, he becomes the third England cricketer to depart a tour with a stress-related illness in recent years.
Former opening batsman Marcus Trescothick left the 2005-06 tour of India and the 2006-07 Ashes tour of Australia, while left-arm spinner Michael Yardy flew home from the 2011 World Cup.
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