The chair of governors at Woodlesford Primary School has said the school community is in "complete shock" over the arrest of Robin Scott.
Parents have also been asked not to discuss the issue on social media.
The Yorkshire Evening Post reported on Friday how Scott has appeared before a magistrates court charged with 10 sex offences involving a teenage boy aged under 16
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The offences are said to have been committed between February 2017 and June 2018.
The 53-year-old is also charged with an offence of meeting the same youngster following grooming between January 2017 and June 2018.
Scott, of Wycar, Bedale, North Yorkshire, is being held in custody over the charges which are alleged to have been committed in Glossop, Derbyshire.
He is due to appear before Derby Crown Court on July 3.
Parents received a text message from the school on Thursday, stating: "Dear parent/carer please note there will be an important letter in your child's bag tonight."
The letter, which was sent to all parents from the school's chair of governors, Jim Ebbs, states: "I am sorry to have to inform you that Mr Scott has been suspended from work with immediate effect due to serious safeguarding allegations that have been made against him involving a young person.
"These allegations relate solely to activity in Derbyshire and there is nothing to suggest that there has been any inappropriate behaviour in school or in the Leeds area.
"Mr Scott is currently being remanded in custody whilst Derbyshire Constabulary conduct a police investigation, which we are supporting them with.
"This news has come as a complete shock to our entire school community.
"I want to reassure you that we have rigourous child protection and safeguarding procedures in place in school, plus safe working practices that ensure the safety and wellbeing of all of our children."
The school also set up meetings for parents to ask questions and to "receive further reassurance."
An acting headteacher has been appointed for the rest of the academic year.
The letter continues: "The police have also asked us to request that everyone refrain from discussing this matter on social media channels as this could have an impact on the outcome of any court case.
"As this is an ongoing police investigation, there is no further information available at this time."
The letter adds: "If you have any cause for concern for your child(ren) of a safeguarding nature, please listen, reassure them that they are safe and come into school in the first instance to speak directly to designated staff."
Scott appeared before Chesterfield Magistrates Court on Tuesday.
The court heard he is accused of initially being in contact with the youngster via social media from when the boy was 13-years-old, according to prosecuting solicitor Becky Allsop.
Mrs Allsop added that when matters allegedly became more sexual the youngster was taken by Scott to a Travelodge.
The defendant, who has not formally entered any pleas, was remanded in custody.
A spokesman for Leeds City Council said: “We have been made aware of a criminal investigation by Derbyshire Constabulary into a member of staff from a Leeds school. The investigation relates to activity in Derbyshire. The member of staff has been suspended with immediate effect.
“We are supporting the school and also Derbyshire Constabulary with their investigation. Due to the ongoing nature of the investigation we are unable to comment further at this time.”