The board of Donaldson's Deaf School, Linlithgow, has taken the unusual step of suspending Janice MacNeill, chief executive, and Mary O'Brien, the head teacher, to establish whether correct procedures were followed in a case dating back to 2009.
The suspension does not mean the board believes there has been any wrongdoing by the two officials, but it is being used as a mechanism to allow an independent investigation to take place.
The move comes four years after an alleged "inappropriate physical act" involving an unnamed member of staff and a young adult not connected with the school.
Although the incident did not happen at Donaldson's, and did not involve any pupils, staff were aware of it, but no action was taken.
When the case was raised at a meeting last term, the school decided further action was required and the member of staff was suspended and police were contacted.
The board of governors of Donaldson's then began an investigation into why appropriate action was not taken sooner, which led to the further suspensions.
Mary Mulligan, convener of the board of governors of Donaldson's, said: "Staff were aware of the 2009 incident at the time, but no official action was taken then.
"Following the decision to contact the police about the incident, the board asked whether the correct child protection procedures had been followed.
"We are now conducting an inquiry to establish whether those procedures were followed and to ensure the correct procedures are in place going forward."
Mrs Mulligan stressed there had been no further allegations against the member of staff, who was a support worker, and no pupils were involved.
A school spokeswoman added: "The board of Donaldson's Trust was recently made aware of certain allegations that we had a duty of care to take seriously.
"In line with due process, and following external advice, we contacted the authorities and a police investigation is under way.
"The individual, who has not been in post for some weeks due to the school summer break, has been suspended pending the outcome of those investigations. It is not possible for us to discuss this matter in any more detail.
"The suspension of two senior members of staff is to allow an internal review only and is not connected to the police investigation.
"The safety and wellbeing of our pupils will always remain a priority for the school."
Donaldson's is Scotland's national school for children who are deaf or have communication difficulties.
A recent inspection of the school graded it as "good" for the quality of care and support, the environment, staff and management and leadership.
The school, which is grant-maintained, was founded in Edinburgh in 1851 as Donaldson's Hospital, but moved to a purpose-built campus in Linlithgow in 2008.