The incident, in which some ceiling tiles and plaster fell to the floor, happened during break time yesterday morning at New Cumnock Primary School in East Ayrshire.
The three children were seen by the school's first aider and it is understood two of them were taken to hospital as a precaution.
The school will be closed for the rest of the week while checks are carried out.
East Ayrshire Council said the safety of its children and staff is "paramount".
A spokeswoman said: "East Ayrshire Council can confirm that New Cumnock Primary School will be closed for the rest of the week.
"This follows an incident in a junior classroom where some ceiling tiles and plaster fell to the floor.
"Closure is to allow further investigation work to continue.
"Parents were immediately informed, in order that they could take their children away for the rest of the day. Three children were attended by the school first aider and subsequently, as a precaution, advised to seek professional medical assurance.
"As always, the safety of our children and members of staff is paramount. Necessary checks will be carried out over the next few days and council officers are set to review the position on Wednesday."