The board of Brindabella Christian College has suddenly sacked the school's principal and warned parents "the devil has his sights on Christian education" as the federal government prepares to legislate for same-sex marriage.
Ousted principal Bruce Handley has taken the school's board to the Fair Work Commission after being booted early this month.
His firing came after a four-page statement was sent to Brindabella parents in September urging a "no" vote in the same-sex marriage survey.
Although Mr Handley's name appeared at the end of the letter, his wife later distanced the family from the document, writing on social media it did not represent her or her husband's views as "we believe Christians can vote 'yes'".
Many parents later contacted The Canberra Times to say they believed Mr Handley did not write the letter.
"The decision came without warning and while I was waiting for the Fair Work Commission to deal with an application for an order to stop bullying that I had filed," Mr Handley said this week.
Board chairman Greg Zwajgenberg, who was in America when the letter was sent, said its contents were written by Christian Education Australia but endorsed and distributed by Mr Handley.
He would not be drawn on why Mr Handley had lost his job but said it was unrelated to same-sex marriage legislation.
To parents, Mr Zwajgenberg wrote: " ... the board of the college has now terminated Mr Bruce Handley's three-year contract one year early, as a component of Bruce's second yearly review.
"Bruce will not be returning to the college in 2018.
"This week we will be advertising nationally for a new dynamic, solid Christian principal to lead the college for the foreseeable future and we will keep everyone informed of our progress."
Mr Handley, an experienced teacher who has held leadership roles in schools throughout Australia and overseas, said it was "obviously a very upsetting time for me and my family".
"There are new proceedings that have now been commenced against the college and that's probably as much as I'd like to say at this time," he said.
A number of parents have pulled their children from Brindabella Christian School since the "no" letter was sent. Two families Fairfax Media spoke with said their children had been subjected to lectures on the same-sex marriage survey and felt alienated after expressing dissenting views.
A letter sent by Mr Zwajgenberg this week confirmed one family's decision to remove their children from the school. The memo asked the school community to keep Brindabella Christian College in its prayers as the devil circled on Christian schools.
"There is a perfect storm coming for Christian education in Australia by way of differing views on clarifications with respect to religious freedoms and the devil has his sights set on Christian education through changing legislation and secular attitudes," Mr Zwajgenberg's letter said.
One parent removing their children from the school said: "We had hoped that a Christian education would involve actively demonstrating love and support for all members of the community.
"The letter sent yesterday showed that the chairman of the board feels Christian education is more about alienating outsiders who are viewed as a threat."
Speaking on Wednesday after the Senate passed a bill in favour of same-sex marriage, Mr Zwajgenberg said Brindabella's position on religious freedoms and same-sex marriage was well-known.
"Our position has always been very clear on Christian teaching and freedoms of religion, so from our particular perspective there's nothing more to add other than Merry Christmas."