The letter in the current edition of Xavier by former student Matt Price, who claims to have been homosexual himself before he was "cured", called for "a world free from homosexuals," the SX news website said.
"The truth will set you free is what Xavier taught me," wrote Price, who now works as a nurse in Queensland.
Gay activist Gary Burns (pictured) wants an apology from the school.
"To publish calls for a world free of homosexuals is nothing less than an incitement to kill gay people," Burns told the website.
Xavier should "apologise unreservedly for this serious and illegal breach of NSW anti-vilification laws".
School headmaster Neville Powles, however, has defended the publication.
"Letters to the editor in any publication are the views of the author and not necessarily the views of the editor or organisation," Powles wrote on the school's website.
"We live in a country where free speech is available to all," he said.
"That said, I apologise for any offence caused ... none was intended."
