Rongotai College has been hit twice in the space of three days.
On the weekend the school's sports changing rooms were tagged.
Then late on Monday night the outside of the school's special needs classroom, brick work and front entry signs were defaced.
Wellington College school principal Gregor Fountain said he and the school's head boy have met with principals, head prefects and caretakers of St Pat's and Rongotai to apologise for the vandalism which took place in the school's name.
"We are appalled that these actions have taken place. These actions in no way reflect the values of the schools involved or Wellington College's positive relationship with the schools that have been targeted."
They were working with police to identify those involved, he said.
Fountain said the four schools have collaborated on several initiatives to ensure the McEvedy Shield was inclusive and a positive experience for everyone.
"We clearly have more work to do."
Rongotai College principal Kevin Carter said camera footage of the offending at his school had been made available to police.
"It took two of our staff the whole day yesterday to remove this from the school. So we've removed it all now and we are getting on with what schooling is about."
"This is a one day athletics event, let it be that."
There had always been a bit of argy-bargy between the schools over the competition but nothing like this, Rongotai MP Paul Eagle.
"I wouldn't want the competition to be stopped but I think now there needs to be a higher level conversation to say guys, if this continues, these are what the consequences look like."
Eagle said the vandalism put a stain on the whole competition, which began in 1922.
"I'm not going to point fingers at any of the schools there must have been a small group who took matters into their own hands who think this is a bit of fun.
"This is certainly not fun. It will cost those schools now to make the repairs."
The McEvedy Shield should be remembered for the spirit of what happened on the field, he said.
Three records were broken at the event held in Newtown Park with Wellington College successfully defending the title for the fifth time.
The schools have been approached for comment.