Neil Bantleman of Burlington, Ont., filed the letter during a hearing Tuesday in the South Jakarta District Court. The letter says he is innocent and the allegations against him are false.
Bantleman and teaching assistant Ferdinant Tjiong, who have been in custody since July, are being tried separately in closed-door sessions.
In the letter, which was emailed to The Canadian Press by Bantleman's brother, the Canadian teacher says the indictment read against him last week left him "deeply saddened and appalled."
He says in the letter that the allegations in the indictment are "baseless and completely false" and that the indictment fails to comply with Indonesian law and should be "rendered null and void."
Bantleman's family says the prosecutor is expected to respond to what is called his application for exception on Thursday and the court is to make a decision the following Tuesday.
Reports say an application for an exception seeks a ruling from the court that the case should be thrown out. The Sydney Morning Herald said that under Indonesian law a case can be dismissed before it begins, but that this is uncommon.
"I am an innocent upstanding member of society," Bantleman says in his letter. "I have never committed any offence against any student or any individual throughout my entire teaching career."
"All of things the indictment letter says, I am not."
Bantleman and his legal team say the prosecutor has not given a specific date, time or location for the alleged incidents.
"The reason that the indictment letter contains no specific date or factual evidence that points to me as a perpetrator, despite six months of investigative work, is simply explained by the fact that I committed no such acts," he says in his letter.
His wife, Tracy Bantleman, echoed his concerns in an phone interview with CHCH news in Hamilton.
"How is somebody supposed to defend themselves?" she asked. "We already know that these crimes never happened, but how possibly can someone even come up with any evidence of being in an alternate location on any one of the days?"
The lack of evidence in general should cause the case to be thrown out, she said.
"If the judges can look at this fairly ... and see that there's issues with procedural law and the fact there's no time and date listed ... then they could very well end up setting a precedent for other cases moving forward, which I think needs to happen in Indonesia," she said.
Bantleman's family says court hearings in the case are expected to continue for the next few weeks.
His legal team is trying to have him transferred out of prison and into house arrest, says his brother Guy Bantleman, adding the court is also expected to decide on this next week.
He says his brother has been harassed by fellow inmates and is concerned for his safety.
Bantleman and Tjiong have continued to maintain their innocence as do fellow teachers and the principal at the Jakarta International School.
A judge read the charges against them in a Dec. 3 session but they were not required to enter a plea.
"After listening to the indictment letter I was deeply saddened and appalled to hear my name associated to claims that I could have in any way carried out such heinous crimes," Bantleman said in his letter.
"My family, the school, and international community are equally offended and distraught to learn of such baseless allegations brought against my good name and character."
Five janitors at the school are being tried over the same allegations. A sixth died in custody.
Guy Bantleman has said while consular officials are providing assistance, the family received a letter from the junior minister responsible for consular affairs, stating Ottawa won't pressure Indonesia to release his brother from jail.
Supporters of Bantleman and Tjiong say the student, who was six at the time the alleged abuse occurred, was subject to suggestive questioning by inexperienced police. The abuse was alleged to have happened at a room in the school during teaching hours.
The family of the student is suing the school for $130 million.
The school in southern Jakarta is attended by the children of foreign diplomats, businesspeople and Indonesia's elite. It has 2,400 students aged three to 18 from about 60 countries.
Bantleman moved to Indonesia four years ago with his wife, who also teaches at the school.
Both Bantleman and Tjiong could face up to 15 years in prison if convicted.
— By Linda Shearman in Toronto
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