A bomb disposal team were called to St Alban's High School in Ipswich following concerns a chemical used in some science lessons were being stored in unsafe conditions.
Sean Salter, business manager at St Alban's, told the Ipswich Star newspaper: "The students were in lessons and half of the school were in an All Saints Day mass in our sports hall.
"The bang was a lot louder than they told me it was going to be. They turned up unannounced, so we had no time to inform anybody."
The blast followed new guidance from CLEAPSS, the Consortium of Local Education Authorities for the Provision of Science Equipment, regarding the storage of chemicals at schools.
In a seperate incident, police were called to Nottingham Academy on Tuesday over fears a quantity of the same substance - 2,4-DNP - was also being stored in unsafe conditions.
Sean Salter from St Alban's also told the Ipswich Star: "We were advised that it can become unsafe if not stored in a particular environment, and the only way it could be disposed of is by a controlled explosion by the bomb squad from Colchester.
"Its got potential to become explosive."