But Flower made it clear Warner's words did not have a direct influence on Trott's exit.
"Jonathan has been struggling with this condition for quite a while and has managed it very successfully but we've been on tour for about a month.
"He's had his ups and downs through that month and it is not directly related to that."
Hugh Morris, managing director of England Cricket, said Trott needed time, support and space to recover.
"The cricket side of things is unimportant now. We fully support his decision to leave the tour and the ECB will provide all the assistance we can to help Jonathan and his family through this period."
Trott said in an ECB statement it wouldn't be right to stay in Australia, given batting was the last thing on his mind.
"I cannot currently operate at the level I have done in the past," said Trott, who made his test debut against Australia in 2009 at The Oval and averages 46.45.
"I want to wish my teammates all the very best for the remainder of the tour. My priority now is to take a break from cricket so that I can focus on my recovery."
- AAP