Institute executive member Virginia Oakly has told the conference in Rotorua that the ministry has agreed to give the communities some extra flexibility.
But a review report, which the institute and the ministry had hoped to sign off last week before the conference, has not yet been agreed on because the ministry has not been willing to "stretch" the model as far as the institute wants.
A main theme at the conference has been that teachers want more support for growing numbers of children who are violent and disruptive because of unsettled home lives, and many schools are reporting children starting school not yet toilet-trained and still in nappies.
Former institute president Louise Green said the institute wanted to use the extra funding for communities of learning "more directly to support children's needs rather than on allowances for a few rigidly prescribed roles".
But the institute "made no progress with the ministry on this issue".
President Lynda Stuart said teachers needed hands-on help from specialists who could work with needy children and their families, freeing the teachers to teach other children in their classes.
"We want to see specialist frontline support that can go in and support teachers and schools - frontline ministry people, psychologists, speech/language therapists, occupational therapists, behaviour specialists," she said.
Education Minister Nikki Kaye announced in August that a new system, aimed at giving each family with a needy child a "single point of contact" to coordinate help from multiple agencies, will be rolled out initially to 30 communities of learning, and 15 ministry staff would be assigned to work across the 30 communities to coordinate the extra help.
But Stuart said the communities of learning were still in set-up mode and were not equipped to take on the coordinating role. She said the extra help should be given to each school directly through special needs coordinators in each school, which is an unfunded role.
"That role is crucial because those are the people in the school who can work with the agencies that the children most need, and work with the family. What we don't need is to take it away from the closest place to the child," she said.
The conference voted to seek variations in teachers' collective agreements and for the ministry to increase flexibility in the use of time and resources in communities of learning, put more focus on roles supporting children with learning challenges, fund time for early childhood teachers to participate in the communities, and allow communities to choose "diverse models of shared leadership".