"No one knows when the final wind up of the world will be," he wrote. "Jesus said no one, only the Father God, knows about that day or hour."
He said Thunberg was a "little girl with self-declared various emotional and mental problems that she thinks give her a special insight into a pending doom".
"She says she is anxious. You too can be anxious. My life experience has taught me that the doomsday predictors are just attention getters," Lynn wrote in his September 26 newsletter.
"Do not be afraid. Your world's future is in the hands of God, not in the predictions of a little girl and false prophets."
The letter was published the same week the 16-year-old made an impassioned speech at the United Nations in New York — hitting out at world leaders for failing to take strong measures to combat climate change.
Galvanised by Thunberg, young people around the world have taken to the streets to demand stronger action on climate change, but Lynn questioned their actions in his letter.
"You can skip school. Hold up a piece of cardboard in the streets and call out for the government to 'do something to stop it all happening' … really???" he wrote.
"Do not be afraid. Your word's future is in the hands of God, not in the predictions of a little girl and false prophets," he wrote before signing off.
"God's promises have never failed yet."
Lynn's letter has been met with some local opposition, with the Coffs Coast Climate Action Group writing on Facebook that "we don't like amplifying the toxic words of this Coffs Harbour principal".
However, the statement went on to say "other more responsible church leaders are calling out his dangerous comments and talking about the need to protect our planet's climate for younger generations".
Another church leader, Dr Greg Jenks — the Dean of Grafton Cathedral — told the ABC Lynn's views were a "horrible expression of Christianity".
"I guess the newsletter is primarily aimed at parents rather than children, but it's a view that encourages people not to take any responsibility for looking after the planet," he said. "It's a complete misuse of scripture, it's a very naive approach."
Since the powerful address at the UN, 16 young people aged eight to 17, including Thunberg, submitted a formal complaint against five countries to the UN under the UN Convention on the Rights of a Child.
Their petition alleged the governments of Argentina, Brazil, France, Germany and Turkey were in violation of the convention through "knowingly causing and perpetuating the climate crisis".
"A scientific consensus shows that the life-threatening risks confronting the petitioners will increase throughout their lives as the world heats up to 1.5°C and beyond," reads the petition. "If the respondents continue their current emissions pathways, the world would warm enough to threaten the lives of billions of children worldwide."
Last week, Thunberg posted a direct message to her trolls, dismissing them as "feeling threatened" by young climate activists and encouraging her followers not to give them the time of day.
News.com.au has contacted Coffs Harbour Christian Community School for comment.
