The Minister for Education was looking after "the general interest" by not assuring Bruce College its fee-paying students would be allowed to sit the Junior Certificate, a spokesman for the Department of Education has said.
Bruce College, which already runs private schools in Dublin, Cork and Limerick for senior cycle students, plans to open Junior Cert centres in each city in September.
However, the Department of Education has refused to assure the college that it will be given permission to have its students sit the exam.
Bruce College applied to become a Junior Certificate exam centre before Christmas, but the Department insists "there is no such thing . . . Only students from recognised schools can sit the Junior Certificate and Bruce College has not applied for recognition.
"It's legitimate for Bruce College to look after its own interests but the Minister also has to look after the general interest," the spokesman said.
Recognised schools receive capitation grants from the State and have a set number of their teachers' salaries paid.
The Minister had been in touch with Bruce College in the last two weeks to tell it he wasn't in a position to give it an answer to its request at the moment, the spokesman said.
Mr Martin was "very surprised Bruce College is advertising the establishment of the school when the decision process is ongoing," he added.
Provisions in the Rules and Programmes for Secondary Schools allowed for certain students to sit the exam outside a recognised school, the spokesman said, but these exceptions were mainly designed to facilitate people on Youthreach and adult education programmes and students who were especially gifted in a subject not available at their school.
