Patricia McGinty, spokeswoman for the Scottish Independent Nurseries Association, said the research showed that private nurseries did well on children's emotional and social development.
"I think the study is making unfair comparisons because the private sector is not just delivering two-and-a-half-hour classes in pre-school education.
We are providing full day care and education for children," Mrs McGinty said.
"Also, local authorities have been doing it so much longer and had the benefit of fully trained staff and teachers. We have done remarkably well in catching up and providing added services for the whole family."
Norma Watson, head of Kirkhill nursery in West Lothian and spokeswoman for the Educational Institute of Scotland, said the findings did not come as a surprise. "It's absolutely crucial you have a trained teacher as head, leading the team. We are highly trained and there is regular access to staff development," she said.
At the Scottish Pre-school Play Association, chief executive Ian McLaughlan acknowledged parent perceptions of a higher quality "education" in nurseries.
"However, there are play leaders in the voluntary sector who draw on many years of experience and are most competent in delivering the same 3-5 curriculum as their colleagues who are teacher trained. Our member groups can also boast of offering lower staff:child ratios."