Two Bishop Vaughan Catholic School pupils have been arrested following enquiries by police.
Neither of the pupils were at the school at the time of the arrests.
A police spokesperson said: "Bishop Vaughan School and South Wales Police have been working together on a sensitive safeguarding issue involving two pupils."
"Following enquiries conducted by the police, two pupils have been arrested.
"Neither of the pupils were at the school at the time of the arrests, which took place at separate addresses on Wednesday morning.
"The safety and welfare of pupils is paramount. The school acted quickly once concerns were raised about the pupils and, with the help of South Wales Police, the issue was quickly resolved without any risk to staff or pupils.
"We would like to reassure parents that the situation has now been resolved and the school is operating as normal.
"Given the confidential nature of the pupil issue, it wouldn't be appropriate for us to comment further at this time.
Police officers are on scene and parents have been spotted picking up their children.The Catholic school on Mynydd Garnllwyd Road in Morriston has around 1,400 pupils aged between 11-18.
A statement which was issued on the school's website by headteacher Paul White read: "As a school we take the Health and Safety of our pupils and staff extremely seriously and have strong, robust safeguarding procedures in place.
"There was a confidential child protection issue this morning and precautionary measures were put in place.
"The situation has now been resolved and the school is operating as normal."