UN officials made clear in the lead-up to the summit that only countries prepared to announce new climate reduction measures would be able to speak at the event.
Later in a tweet,Trump said of Thunberg,"She seems like a very happy young girl looking forward to a bright and wonderful future. So nice to see!"
Andrew Highman,the chief executive of global climate action lobby group Mission 2020,said representatives from other countries had noticed Australia's absence from the high-powered event.
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"It is really very obvious who is absent from the room,"he said.
"Everyone is well aware that Australia has not made good on its promises in Paris to scale up its commitment to climate action."
UN Secretary-General Antonio Guterres urged world leaders to move with more urgency before a major climate change meeting in Santiago,Chile,in December.