The survey for people aged nine to 17 - and their parents, carers and grandparents - asks for stories about how COVID-19 has affected them and how they are coping.
As most Australian children head back to school on Monday they are being asked to include stories about their return particularly amid the summer Omicron outbreak.
National Children's Commissioner Anne Hollonds says children and parents sharing their experiences will help governments improve support services.
"Children and young people have not had many opportunities to be heard during the pandemic," she said.
"The surveys will consider the social, emotional, educational, and other impacts children and young people have experienced over the past two years."
Before the COVID-19 pandemic Australian children were already experiencing a mental health crisis.
Indications are that missed school, social isolation, increased anxiety and other impacts of the pandemic have exacerbated the crisis.
"Understanding these impacts in greater detail will help governments design better services to support the mental health and wellbeing of children and young people," Ms Hollonds said.
In addition to the children's survey, parents, grandparents and carers are being invited to complete a second survey, to capture their experiences and perspectives about the pandemic's impact on children and their families.
Both surveys are strictly confidential and funded by the National Mental Health Commission.
They are available at www.kidscovidsurvey.com and the Australian Human Rights Commission will report the results later this year.
Lifeline 13 11 14
Kids Helpline 1800 55 1800 (for people aged 5 to 25)
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