Mr Thornton said the trial was being run together with a company, Education Perfect.
It was one of several projects being undertaken by NZQA to test the waters of moving real exams and assessments online.
The authority wants to eventually convert end-of-year NCEA secondary school exams to a test-as-you-learn online format.
"Feedback from the students and teachers as to the format of the assessment will also inform any future work/development around digital assessments."
NZQA chief executive Dr Karen Poutasi has previously told the Herald that her staff were watching developments in online assessment at the university level.
She said the NCEA exam system involved 2 million pieces of paper moving round the country, and encouraged online learning but sent students "back to the Dark Ages" to hand-write exams.
President of the Post Primary Teachers Association Angela Roberts told the Herald she was opposed to the idea of a private company being used to deliver school exams.
News of the pilot was first posted on Education Perfect's website.
"That is a clear example of when you start contracting out what I would consider your core business, you start losing control.
"And we get nervous about that in education, we are incredibly sensitive to how easily things can go wrong when you contract out - when you look at Novopay, for example."