Nicholas Conlon Smith, 36, is in the Wake County jail. His bond is now set at $2 million.
According to a bio on the school's website which has since been taken down, Smith taught at the school for 12 years and was the math director at the middle and upper school.
The alleged offenses happened with a 14-year-old student between August of 2011 and June of 2012.
The head of the school, Nancy Errichetti, issued a statement Tuesday.
"There is nothing more important than the safety of our students. These allegations are extremely disturbing and we are cooperating fully with the police investigation. We will also conduct a comprehensive review of our own policies and procedures as part of our ongoing commitment to protect our students," she said.
A prosecutor said Wednesday there could be more charges and asked for the bond increase from one to two million dollars.
"In this particular case there are numerous counts, two different victims, and all indications are that there may be more charges coming as well from a different county," said Wake County Assistant District Attorney Christy Joyce.
Bond doubled for Montessori School of Raleigh teacher accused of having sex with a student after prosecutor tells judge there’s a second victim and more charges may be coming. #ABC11 pic.twitter.com/F862AmKuNn— Ed Crump (@EdCrumpABC11) November 8, 2017