Addressing the AGM of the Catholic Primary School Manager's Association the minister criticised what he called scaremongering carried out by some Catholic schools during a recent survey of parents to measure the need for change.
Mr Quinn said he had heard of campaigns operated by some schools during the survey process that claimed there would be a unilateral handing over of Catholic schools to non-Catholic parents.
The Minister called this regrettable.
Ruairi Quinn said he fully supported the framework, as outlined by the church, which saw new arrangements for diversity of choice in place by September 2014.
Mr Quinn told Catholic school managers he hoped the final responses of the bishops, due in October, would pave the way for greater diversity in 29 areas around the country.
On the subject of the time allocated to the teaching of religion in schools, Mr Quinn said recent OECD figures suggested that Ireland and Israel spend considerably more time than any other OECD countries on religious instruction in schools.
He called for public discussion on the matter.
Meanwhile, the CPSMA has called on the minister to restore, as a matter of urgency, a grant that enabled schools to carry out small but vital repairs.
At its AGM the CPSMA said 67% of Primary schools were now in deficit as a result of the abolition of the Minor Works Grant.
The Association's Deputy President Fr Denis McNelis said a primary school with 100 mainstream pupils and five special needs pupils had lost 20% of its funding in recent times, the equivalent of almost €10,500.