It says grades awarded last week are provisional and subject to change depending on the outcome of the investigation.
But deputy head Barry Phillips said the decision to withhold the marks from all 280 GCSE maths candidates was unfair. He believes the exam board's concerns about coursework relate to only one pupil.
Pupils were said to be devastated after the marks for coursework, accounting for 20 per cent of the final grade, were deducted.
The school is due to meet with the exam board in the second week of term.
Letters have gone out to parents explaining why grades were lower than anticipated and inviting them to a meeting on Monday. Mr Phillips said the school hoped for a satisfactory outcome before the end of the month and the awarding of certificates. He said: "It's a shame that the pupils' grades did not reflect the coursework. It has had a devastating effect on the school's overall A*-C results."
Sixteen-year-old Lynette Lisle was given a D grade in her maths GCSE without her coursework added. She passed her other subjects at grades A*-C - including two A*s. She said: "I'm confident it will rise to a C after the coursework is added on."
Forty-four schools and colleges in Wales use OCR as an examining body for maths. Spokesperson Jennifer Roberts said the investigation at Fitzalan high was the only one in Wales.
She said: "OCR can confirm there is an on-going investigation into the conduct of GCSE mathematics coursework at the school."