Boyle confirmed that disciplinary investigations had been undertaken, but said it was important that there was a "fair and thorough" investigation.
"This school has a strong sense of reponsibility to ensuring the well-being and welfare of all boys at all times including when they get it wrong."
St Bede's board of trustees and the rector took ultimate reponsibility for the boys and their behaviour when they were representing the school, he added.
The misconduct follows previous drama in 2015, when St Bede's rowers Jack Bell and Jordan Kennedy were barred from the Maadi Cup after breaching security at Auckland Airport.
The row was sparked after the two boys were caught riding on the baggage conveyor at Auckland Airport's domestic terminal.
In that instance, St Bede's also ruled that the pair breached the school's code of conduct, but the families of two boys successfully sought a High Court injunction to allow their sons to compete.
In 2014, eight St Bede's boys were involved in an incident at the Maadi Cup in Twizel which allegedly included dousing tennis balls in petrol and setting them alight before throwing them. They were also accused of pouring petrol on the road to spell out "SBC" and drawing the shape of a penis and lighting it so it burned into the road.
The boys were banned from attending the regatta's social events and made to carry out community service in the town during school holidays, but were allowed to compete in the regatta.
St Bede's did not win any medals at the 2017 Maadi Cup.