Chef de mission Chiller also criticised Tennis Australia for backing Kyrgios, saying she found it "difficult" to accept that the governing body could regard the hot-headed 21-year-old an "athlete of good standing".
Kyrgios withdrew his name from consideration for Rio on Friday and blamed the Australian Olympic Committee for "unfair and unjust treatment" after a row with Chiller over his conduct.
Chiller rejected Kyrgios's comments and said the AOC had reached out to the player, asking him to respond to a letter about their concerns.
"He was sent a letter, as were two other people, asking him to basically please explain and he chose to respond in this way," Chiller said of Kyrgios's withdrawal in a TV interview on Saturday.
"If Nick had have chosen to respond to this letter, that would then go to the full AOC executive to determine (his selection for Rio).
"My personal opinion, I think the damage was done."
After being publicly upbraided about his behaviour by Chiller last month, Kyrgios bowed out of the third round of the French Open with a string of code violations, including one for yelling at a ball-boy.
Despite that, Tennis Australia has defended Kyrgios throughout the Olympic row and the governing body's president Steve Healy said he had shown "growing maturity".
"But we are very disappointed that he has been put in this position," Healy said in a statement after Kyrgios's withdrawal.
Chiller said her relationship with TA was "fine" but felt the governing body were wrong on Kyrgios.
"I think they could have handled it a little bit better, also," she told local broadcaster Channel Seven.
"I’m very surprised with the statement Tennis Australia put out yesterday supporting Nick. For Tennis Australia to say he was an athlete of good standing, I find difficult."
Kyrgios's withdrawal comes weeks after compatriot Bernard Tomic confirmed he would skip the Games over scheduling.
Tomic was also warned by Chiller about his on-court conduct.
The loss of Australia's two greatest medal hopes has heaped further scorn on the players from a disappointed public but also prompted criticism of Chiller and the Olympic committee for being over-bearing.
Tennis great Rod Laver urged critics to lay off Kyrgios.
"If we can encourage him and not criticise is probably the best thing that can happen right now," the 77-year-old Australian said in comments published by News Ltd media.
"I think all this criticism, it's like waving a red rag at a bull.
"The more he hears it, the more he's going to be critical of everything -- and nobody wins.
"We need him to keep going and become a great player."
(Reporting by Ian Ransom; Editing by Nick Mulvenney/Amlan Chakraborty)
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