The Herald believes a complaint made to the school about the conduct came from the boy's girlfriend, a former student at the high school.
The school's principal confirmed that the school board of trustees last month wrote to the teacher, who is understood to be married with at least one child, outlining allegations of "overstepping professional boundaries". "It appears that she may have given significant support to some students ahead of others, and that is of concern to us," the principal said.
He stressed there was no evidence or suggestion of sexual relations between the teacher and any of her students and that she was not suspended. However, the school could not progress the matter until the teacher responded to the allegations.
When contacted at her home by the Herald, the teacher declined to comment.
The principal said initially the PE head of department observed "incidents" that could have been favouritism after which "expressions of concern" were made by the former student.
He said the school was only dealing with incidents that occurred at school and could not comment on the allegations of gifts and outside-school contact.
Before the allegations the teacher was a "good classroom teacher" and there had never been any issues in her six-year history at the school, the principal said.
"We are in the process of going through the assessments that have been marked by her to ensure that the marks and the grades that the students get reflect accurately the work that they have done."
He would not say if any grades had changed but the Herald understands at least one student is facing a downgrade from "merit" to "achieved".
One parent became concerned about the teacher's interaction with her Year 13 son when she found a Facebook message from her coaching the boy's response to school inquiries over some minor trouble a group of students were in.
"I expect a phone call, not that a teacher is Facebooking my son behind my back."
The matter had not been reported to the Teachers Council, a spokesman said, and the Ministry of Education had not received any complaints about a teacher at the high school.
Teacher case
*PE teacher accused of favouritism.
*School remarking a year of NCEA grades.
Other allegations include:
*Outside-school contact.
*Use of a fake Facebook profile to communicate with a student.
*Giving gifts to at least one student.