"The comment was racist and offensive and as a community we are shocked and saddened that a group was targeted in this manner."
Both times, the graffiti had been immediately removed and the toilets had been closed.
The comments had been photographed and handed to the police, the Ministry of Education had also been notified.
In the letter, the school apologised to Pacific students, saying their right to have a safe learning environment had been disrupted.
Support had been offered to affected students.
A video message from a group of Pacific student leaders at the school was also presented at an assembly last week.
The acting principal of Wellington Girls' College declined to be interviewed.