Mr Lynn appeared to question the actions of teenagers who took part in a global climate strike, writing: "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???"
While he never named Ms Thunberg in the piece, the principal wrote:
"You can listen to a little girl with self-declared various emotional and mental problems that she thinks give her a special insight into a pending doom of 'climate change'.
"She says she is anxious. You too can be anxious."
The teen has previously described living with Asperger syndrome, which falls on the autism spectrum, as a gift because it helps her "see things from outside the box".
Mr Lynn said "doomsday ideas" came from attention seekers, including "a little girl from Scandinavia", and that he was introduced to the same "waffle talk" in high school and it never happened.
"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."
Source: Coffs Harbour Christian Community School
The Coffs Coast Climate Action Group wrote on Facebook that, "we don't like amplifying the toxic words of this Coffs Harbour principal".
But it said, "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".
Others have criticised Mr Lynn's comment on social media.
"Enough of this old generation. At least the kids doing the strikes are thinking more about the world than themselves as individuals," one user wrote on Facebook.
Another said, "it's nice to know what he thinks of kids on the spectrum. I will be crossing this school off my list".
Mark Spencer of Christian Schools Australia said Christian schools broadly "are concerned for God's creation".
"Our member schools generally would have a very strong view of taking care of God's creation ... It's fundamental to what we believe as Christians," he told SBS News.
"We talk about 'creation care'. It's something that all our schools seek to do. Different schools have a lot of initiatives around educating children on environmental issues ... Both at a practical level such as recycling programs at school or more generally as part of the curriculum."
He stressed that Coffs Harbour Christian Community School used to be part of his organisation but is not any more.
A UN report released last month found climate change is accelerating, with carbon dioxide levels increasing, sea levels rising and ice sheets melting faster than ever.
SBS News has contacted the school for comment.