Team coach Andy Flower revealed that England's number three batsman has been suffering from stress and has felt unable to continue playing.
"He's been suffering from a stress-related condition for quite a while," said Flower.
"He's been struggling with this condition for quite a while and managed it very successfully.
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"We had high hopes that Trotty would have a great tour but it hasn't worked out that way. Hopefully he will come back stronger."
Trott released a statement explaining his decision.
""I don't feel it is right that I'm playing knowing that I'm not 100% and I cannot currently operate at the level I have done in the past,” he said.
"My priority now is to take a break from cricket so that I can focus on my recovery. I want to wish my team-mates all the very best for the remainder of the tour."
Australian star David Warner had launched a withering attack on Trott at the weekend, sledging him remorselessly at the crease and saying at the end of play that Trott had "scared eyes" and calling him "poor and weak".
Flower refused to blame Warner for Trott pulling out of the series, but had harsh criticism for the controversial Aussie, who was banned during the summer Ashes series for punching Joe Root in a bar.
"I would say that players commenting about fellow professionals in the media is horribly disrespectful," Flower said. "On this occasion I think he's got that wrong."
Warner himself had already admitted that he had overstepped the mark: "Probably went a little bit too far with the comments, but it's cricket," he said, adding, "now it's in the back of their mind."
Prominent cricket broadcaster David Lloyd, who played nine Tests for England as an all-rounder, also singled out 27-year-old Warner for going overboard with his on-field chatter.
"I'm a big lad who has heard a few things in my time but David Warner in particular came out with some really nasty, horrible stuff," Lloyd wrote in the Daily Mail about comments picked up by broadcaster Sky's stump microphone.
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