The ministry says the numbers are necessary as they give it an accurate picture of enrolment, attendance and teaching at ECE centres.
There were fears within the ECE sector about how children's information might be used but they have largely been allayed after assurances and monitoring by the Privacy Commissioner.
However, Gloriavale is still opposed and a transition period set by the ministry is coming to an end. No other provider has refused to use the numbers.
"National student numbers are used to record data [and] specifically to protect a child's privacy. It allows us to identify a child without having to refer to names or addresses," said Katrina Casey, the ministry's head of sector enablement and support.
"Gloriavale ... disagree with the use of a student number for their children. We visited them last year and most recently last month to discuss their concerns."
Ms Casey, who would not reveal what exactly Gloriavale's concerns were, said the ministry would continue to work on a solution, but had explained that ECE funding "is likely to be put at risk". "That would be the same for any other ECE provider."
The Education Review Office (ERO) in June awarded Gloriavale's three "Garden of Children" early childhood centres the highest grade of being "very well placed".
Ms Casey said there were 152 children enrolled at the centres and between July 2014 and June 2015 they received ECE funding of $2,403,844.
Gloriavale spokesman Fervent Stedfast, when asked if the 530 strong community objected to using national student numbers, had no comment to make.
Catherine Delahunty, education spokeswoman for the Green Party, has said she is concerned Gloriavale students appear to be pressured into completing NCEA early so they can work in the community.
ERO officials will appear before a select committee next week, and will face questioning over the office's positive assessment of Gloriavale's schooling.