The two events were separate, according to Gary Cregan, principal of St. Anthony's High School.
The boys allegedly brought the flag to a school gathering on April 9. Teachers immediately took it away, and the students were suspended.
Two days later on Friday, the girls posted a photo of one of them in blackface, along with racist language, the school confirmed.
In a letter to parents on Friday about the flag incident, Cregan said the use of symbol "designed to revive past injustices or to inflame discrimination or racial intolerance is completely unacceptable and profoundly offensive."
"St. Anthony's will always demand acceptance and respect for all races, religions and cultures," he wrote.